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Created on: 11-Apr-2011   Last updated on: 20-Dec-2011  |  How to cite this?
Total resources - 350
A compilation of protein-protein interaction resources
Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
ADVICE - Automated Detection and Validation of Interaction by Co-Evolution
http://advice.i2r.a-star.edu.sg
Predicts and validates protein-protein interactions using the observed co-evolution between interacting proteins. Protein sequence or list of sequences to be used as input. Interactions can be restricted to given experimental evidence.
"Tan SH, Zhang Z, Ng SK. ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W69-72. PubMed PMID: 15215353; PubMed Central PMCID: PMC441609."
2004
1
ANCHOR
http://structure.pitt.edu/anchor
A web-resource that predicts protein interactions based on the domain/interfaces/sites. Provides the kinetics/thermodynamics of the interactions. User interface parameters can be implied to the input. Provides interactions at amino acid level. Provides protein-small molecule interactions.
"Meireles LM, Dömling AS, Camacho CJ. ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W407-11. Epub 2010 Jun 4. PubMed PMID: 20525787; PubMed Central PMCID: PMC2896143."
2010
32
BioGRID - Biological General Repository for Interaction Datasets
http://thebiogrid.org
A database that provides genetic interactions along with PPIs. Categorizes the interactions based on the evidence score. Provides interactions for a given PMID of article. Interactions can be restricted to given experimental evidence.
"Breitkreutz BJ, Stark C, Tyers M. The GRID: the General Repository for Interaction Datasets. Genome Biol. 2003;4(3):R23. Epub 2003 Feb 27. PubMed PMID: 12620108; PubMed Central PMCID: PMC153463."
2003
48
ATTED-II
http://atted.jp
"A database of gene co-expression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. It also integrates known PPI information on co-expressed gene network."
"Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9. Epub 2006 Nov 27. PubMed PMID: 17130150; PubMed Central PMCID: PMC1716726."
2006
79
AnimalTFDB - Animal Transcription Factor DataBase
http://www.bioguo.org/AnimalTFDB
"A comprehensive Transcription Factor (TF) database which has identified and classified all the genome-wide TFs in animal genomes. The TF identification is based on the 'Hidden Markov Model' of their DNA-binding domains. It provides general annotation information for all the TFs, transcription co-factors and chromatin remodeling factors in the database, including protein interactions."
"Zhang HM, Chen H, Liu W, Liu H, Gong J, Wang H, Guo AY. AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res. 2011 Nov 12. [Epub ahead of print] PubMed PMID: 22080564."
2011
94
AVID - Annotation Via Integration of Data
http://web.mit.edu/biology/keating/AVID
"A method for predicting functional relationships among proteins. It integrates the results of high-throughput experiments, and incorporates sequence data, to build unified, high-confidence networks in which proteins are connected based on their common annotation."
"Jiang T, Keating AE. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics. 2005 Jun 1;6:136. PubMed PMID: 15929793; PubMed Central PMCID: PMC1177925."
2005
94
2P2I(DB)
http://2p2idb.cnrs-mrs.fr
A database of protein-protein/protein-ligand/protein-inhibitor interactions. 3D view of the PPI data. User interface parameters can be implied to the input.
"Bourgeas R, Basse MJ, Morelli X, Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One. 2010 Mar 9;5(3):e9598. PubMed PMID: 20231898; PubMed Central PMCID: PMC2834754."
2010
96
Babelomics
http://www.babelomics.org
"An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. It integrates various analysis tools including tools for PPI annotation."
"Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4. PubMed PMID: 15980512; PubMed Central PMCID: PMC1160217."
2005
96
ADAN - Prediction of protein-protein interActions of moDular domAiNs
http://adan-embl.ibmc.umh.es
A platform for prediction of protein-protein interaction of modular domains. Provides protein-ligand interactions. Identifies the protein interactions for a given PMID.
"Encinar JA, Fernandez-Ballester G, Sánchez IE, Hurtado-Gomez E, Stricher F, Beltrao P, Serrano L. ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs. Bioinformatics. 2009 Sep 15;25(18):2418-24. Epub 2009 Jul 14. PubMed PMID: 19602529."
2009
97
CEZANNE - Co-Expression Zone ANalysis using Networks
http://acgt.cs.tau.ac.il/matisse/#cezanneref
A novel methodology for extracting sub-networks with correlated expression profiles (co-expression modules) that uses a confidence-based interaction network.
"Ulitsky I, Shamir R. Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics. 2009 May 1;25(9):1158-64. Epub 2009 Mar 17. PubMed PMID: 19297352."
2009
97
"AMEN - Annotation, Mapping, Expression and Network"
http://sourceforge.net/projects/amen
"A stand-alone, unified suite of tools to manage, explore and combine high-throughput data such as annotation, chromosomal location, expression and interaction data. "
"Chalmel F, Primig M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics. 2008 Feb 6;9:86. PubMed PMID: 18254954; PubMed Central PMCID: PMC2375118."
2008
98
AVIS - AJAX viewer of interactive signaling networks
http://actin.pharm.mssm.edu/AVIS2
"A visualization tool, that helps in viewing and sharing intracellular signaling, gene regulation and protein interaction networks."
"Berger SI, Iyengar R, Ma'ayan A. AVIS: AJAX viewer of interactive signaling networks. Bioinformatics. 2007 Oct 15;23(20):2803-5. Epub 2007 Sep 12. PubMed PMID: 17855420; PubMed Central PMCID: PMC2724864."
2007
98
BIND/BOND - Biomolecular Object Network Databank
http://bond.unleashedinformatics.com
"A database of protein-domain/ domain-domain interactions. Provides PPIs for a specific disease (e.g., prostate cancer). Provides protein-small molecule, protein-nucleic acid & genetic interactions. Provides the interactions along with the complexes and pathways involved. Also provides viral-human protein interactions (e.g., HIV-host protein interactions). "
"Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res. 2001 Jan 1;29(1):242-5. PubMed PMID: 11125103; PubMed Central PMCID: PMC29820."
2001
98
BioLayout
http://www.biolayout.org
"A gene expression (GE) analysis tool, that analyzes the GE data and its networks, including PPIs."
"Enright AJ, Ouzounis CA. BioLayout--an automatic graph layout algorithm for similarity visualization. Bioinformatics. 2001 Sep;17(9):853-4. PubMed PMID: 11590107."
2001
98
CCDB - Cell Cycle Database
http://www.itb.cnr.it/cellcycle
A database of genes and proteins involved in human and yeast cell cycle. It provides several information related to these genes/proteins including protein-interactions.
"Alfieri R, Merelli I, Mosca E, Milanesi L. A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst Biol. 2007 Aug 1;1:35. PubMed PMID: 17678529; PubMed Central PMCID: PMC1995223."
2007
98
3DID - 3D interacting domains
http://3did.irbbarcelona.org
A resource that provides domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. Provides domains associated with Gene Ontology terms. Provides information of the interacting motifs for a queried sequence.
"Stein A, Russell RB, Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D413-7. PubMed PMID: 15608228; PubMed Central PMCID: PMC539991."
2005
99
aMAZE
http://www.amaze.ulb.ac.be
A platform for analysis of biochemical and signaling pathway networks. Predicts protein interactions based on gene expression. Provides protein-small molecule interactions.
"Lemer C, Antezana E, Couche F, Fays F, Santolaria X, Janky R, Deville Y, Richelle J, Wodak SJ. The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D443-8. PubMed PMID: 14681453; PubMed Central PMCID: PMC308873."
2004
99
APID/APIN - Agile Protein Interaction DataAnalyzer
http://bioinfow.dep.usal.es/apid
"A protein interaction data analyzer of currently known information about PPIs. Metadatabase (integrates PPI data from multiple resources). Provides Gene Ontology (GO) terms / common GO terms to PPIs (i.e., interactors). Interactions can be restricted to a given experimental evidence."
"Prieto C, De Las Rivas J. APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W298-302. PubMed PMID: 16845013; PubMed Central PMCID: PMC1538863."
2006
99
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana
http://www.functionalnet.org/aranet
"A resource of interactions in plant proteins (Arabidopsis thaliana). Provides both experimental & predicted interactions. Provides interactions based on the proteins' sequence conservation/similarity. Provides functional associations for the interactions. Provides the pathway and other proteins involved, along with the interactions, for a given set of proteins. Predicted interaction based on gene expression. Provides interactions along with their functional associations. Interactions can be restricted to a given experimental evidence."
"Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol. 2010 Feb;28(2):149-56. Epub 2010 Jan 31. PubMed PMID: 20118918; PubMed Central PMCID: PMC2857375."
2010
99
AtPID - Arabidopsis thaliana Protein Interactome Database
http://www.megabionet.org/atpid
"A database of interactions in plant proteins (Arabidopsis thaliana). Provides predicted interactions based on gene expression, genomic data, Gene Ontology terms, orthology. Provides domain interactions. Provides functional associations for the interactions."
"Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008. Epub 2007 Oct 25. PubMed PMID: 17962307; PubMed Central PMCID: PMC2238993."
2007
99
AtPIN - Arabidopsis thaliana protein interaction network
http://bioinfo.esalq.usp.br/atpin
A database of interactions in plant proteins (Arabidopsis thaliana). Provides functional associations for the interactions. Allows to search and build interaction networks based on publicly available PPI datasets.
"Brandao MM, Dantas LL, Silva-Filho MC. AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics. 2009 Dec 31;10:454. PubMed PMID: 20043823; PubMed Central PMCID: PMC2810305."
2009
99
BioProfiling.de - Analytical Web portal for High-throughput biology
http://www.BioProfiling.de
"A free web portal for analyses and interpretation of gene/protein lists.The list is profiled with respect to the most information available regarding gene function, protein interactions, pathway relationships, in silico predicted microRNA to gene associations, as well as, information collected by text mining."
Antonov AV. BioProfiling.de: analytical web portal for high-throughput cell biology. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W323-7. Epub 2011 May 23. PubMed PMID: 21609949; PubMed Central PMCID: PMC3125774.
2011
99
CABIN - Collective Analysis of Biological Interaction Networks
http://www.sysbio.org/dataresources/cabin.stm
A PPI analysis tool. Integrates PPI data from multiple sources and provides prediction with high confidence.
"Singhal M, Domico K. CABIN: collective analysis of biological interaction networks. Comput Biol Chem. 2007 Jun;31(3):222-5. Epub 2007 Mar 30. PubMed PMID: 17500038."
2007
99
CADgene - Coronary artery disease gene database
http://www.bioguo.org/CADgene
"A manually curated database for coronary artery disease genes and associated information such as the size of case-control, population, SNP, odds ratio, P-value. The annotations include general gene information, Gene Ontology annotations, KEGG pathways, PPIs (from BioGrid and HPRD) and others."
"Liu H, Liu W, Liao Y, Cheng L, Liu Q, Ren X, Shi L, Tu X, Wang QK, Guo AY. CADgene: a comprehensive database for coronary artery disease genes. Nucleic Acids Res. 2011 Jan;39(Database issue):D991-6. Epub 2010 Nov 2. PubMed PMID: 21045063; PubMed Central PMCID: PMC3013698."
2010
99
CAPIH - Comparative Analysis of Protein Interactions for HIV-1
http://bioinfo-dbb.nhri.org.tw/capih
"A server that provides protein interactions between human and three major animal models: chimpanzee, Rhesus macaque, and mouse. Also provides the regulation of interaction and also orthologous events."
"Lin FK, Pan CL, Yang JM, Chuang TJ, Chen FC. CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. BMC Microbiol. 2009 Aug 12;9:164. PubMed PMID: 19674441; PubMed Central PMCID: PMC2782265."
2009
99
CastorDB
http://castordb.msubiotech.ac.in
"A specialized and comprehensive database for the oil seed plant Ricinus communis (castor), integrating information from several diverse resources. It contains information on gene and protein sequences, gene expression and Gene Ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, it has used computational analysis to predict cellular localization, domains, pathways, PPIs, sumoylation sites and biochemical properties and has been included as derived data."
"Thakur S, Jha S, Chattoo BB. CastorDB: a comprehensive knowledge base for Ricinus communis. BMC Res Notes. 2011 Sep 13;4:356. PubMed PMID: 21914200; PubMed Central PMCID: PMC3184282."
2011
99
3D-Garden - Global and Restrained Docking Exploration Nexus
http://www.sbg.bio.ic.ac.uk/3dgarden
"An integrated software suite for performing protein-protein and protein-polynucleotide docking. For any pair of biomolecules structures specified by the user, it generates an ensemble of putative complexed structures and rank them. The highest-ranking candidates constitute predictions for the structure of the complex. Complexes of protein and nucleic acid chains can also be specified as individual interactors for docking purposes."
"Lesk VI, Sternberg MJ. 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics. 2008 May 1;24(9):1137-44. Epub 2008 Mar 7. PubMed PMID: 18326508."
2008
100
3D-Interologs
http://3d-interologs.life.nctu.edu.tw
"A resource that predicts evolution of protein-protein interactions across species based on ""3D-domain interolog mapping"". Gets similar protein interactions among species. Provides interactions along with their functional associations."
"Lo YS, Chen YC, Yang JM. 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. BMC Genomics. 2010 Dec 1;11 Suppl 3:S7. PubMed PMID: 21143789; PubMed Central PMCID: PMC2999352."
2010
100
ABAC database
http://scoppi.biotec.tu-dresden.de/abac
A database of protein-protein complexes involving homologous proteins in interaction with different partners.
"Henschel A, Kim WK, Schroeder M. Equivalent binding sites reveal convergently evolved interaction motifs. Bioinformatics. 2006 Mar 1;22(5):550-5. Epub 2005 Nov 15. PubMed PMID: 16287935."
2005
100
ADHESOMEFANetwork
http://www.adhesome.org
A database of interactions composing the focal adhesion complex in mammalian cells.
"Zaidel-Bar R, Itzkovitz S, Ma'ayan A, Iyengar R, Geiger B. Functional atlas of the integrin adhesome. Nat Cell Biol. 2007 Aug;9(8):858-67. PubMed PMID: 17671451; PubMed Central PMCID: PMC2735470."
2007
100
AliBaba
http://alibaba.informatik.hu-berlin.de
"An interactive tool that parses PubMed abstracts and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search."
"Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U. AliBaba: PubMed as a graph. Bioinformatics. 2006 Oct 1;22(19):2444-5. Epub 2006 Jul 26. PubMed PMID: 16870931."
2006
100
AntiJen
http://www.darrenflower.info/antijen
A resource that provides PPIs related to immune system. Provides an option to BLAST the input sequence.
"Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR. AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res. 2005 Oct 6;1(1):4. PubMed PMID: 16305757; PubMed Central PMCID: PMC1289288."
2005
100
APID2NET
http://bioinfow.dep.usal.es/apid/apid2net.html
"An open access tool, included in Cytoscape, that allows to surf unified interactome data by quering APID server and facilitates dynamic analysis of the PPI networks. It is designed to visualize, dynamically explore and analyze the proteins and interactions retrieved, including all the annotations and attributes associated to such PPIs, i.e.: Gene Ontology terms, Pfam and InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs, etc. "
"Hernandez-Toro J, Prieto C, De las Rivas J. APID2NET: unified interactome graphic analyzer. Bioinformatics. 2007 Sep 15;23(18):2495-7. Epub 2007 Jul 21. PubMed PMID: 17644818."
2007
100
ARNIE - AVEXIS Receptor Network with Integrated Expression
http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie
"A database that integrates the extracellular protein interaction network generated in the ""Wellcome Trust Sanger Institute"" using AVEXIS technology with spatiotemporal expression patterns for all genes in the network."
Not available
Not available
100
Bacteriome.org - Bacterial protein interaction database
http://www.bacteriome.org
"A web-resource that provides domain interactions along with PPIs. Provides protein interactions along with the complexes involved. Protein interactions specific to a biological process (e.g., apoptosis, cell cycle) can also be obtained. Provides interactions along with their structural relationships."
"Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J. Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res. 2008 Jan;36(Database issue):D632-6. Epub 2007 Oct 16. PubMed PMID: 17942431; PubMed Central PMCID: PMC2238847."
2007
100
BIANA - Biologic Interactions and Network Analysis
http://sbi.imim.es/web/BIANA.php
"A tool for biological information integration and network management. It has two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges."
"Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics. 2010 Jan 27;11:56. PubMed PMID: 20105306; PubMed Central PMCID: PMC3098100."
2010
100
BID/wikiBID - Binding Interface Database Wiki
http://tsailab.chem.pacific.edu/wikiBID
"A resource that provides interactions related to proteins with mutation information. Provides the negative design elements (mutation that causes proteins to interact better at a lower energy). Protein interactions specific to a biological process (e.g., apoptosis, cell cycle) can also be obtained. Provides the kinetics/thermodynamics of the interactions."
"Fischer TB, Arunachalam KV, Bailey D, Mangual V, Bakhru S, Russo R, Huang D, Paczkowski M, Lalchandani V, Ramachandra C, Ellison B, Galer S, Shapley J, Fuentes E, Tsai J. The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics. 2003 Jul 22;19(11):1453-4. PubMed PMID: 12874065."
2003
100
Bio::Homology::InterologWalk
http://search.cpan.org/~ggallone/Bio-Homology-InterologWalk
"A Perl module to retrieve, prioritise and visualise putative PPIs using interolog mapping. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an ""Interaction Prioritization Index"" that can be used to help prioritize interologs for further analysis."
"Gallone G, Simpson TI, Armstrong JD, Jarman AP. Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. BMC Bioinformatics. 2011 Jul 18;12:289. PubMed PMID: 21767381; PubMed Central PMCID: PMC3161927."
2011
100
BioDrugScreen
http://www.biodrugscreen.org
Drug design /Docking tool.
"Li L, Bum-Erdene K, Baenziger PH, Rosen JJ, Hemmert JR, Nellis JA, Pierce ME, Meroueh SO. BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome. Nucleic Acids Res. 2010 Jan;38(Database issue):D765-73. Epub 2009 Nov 18. PubMed PMID: 19923229; PubMed Central PMCID: PMC2808957."
2009
100
BiologicalNetworks/IntegromeDB/PathSys
http://biologicalnetworks.net
A resource that provides PPIs for a given set of genes. Also identifies other relationships among the genes. Can build pathways with a set of genes.
"Baitaluk M, Sedova M, Ray A, Gupta A. BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W466-71. PubMed PMID: 16845051; PubMed Central PMCID: PMC1538788."
2006
100
BioNetBuilder
http://err.bio.nyu.edu/cytoscape/bionetbuilder
A resource that provides PPIs for a given set of genes. Provides protein-DNA and protein-RNA interaction. Also provides the Gene Ontology terms of the proteins.
"Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R. BioNetBuilder: automatic integration of biological networks. Bioinformatics. 2007 Feb 1;23(3):392-3. Epub 2006 Nov 30. PubMed PMID: 17138585."
2006
100
BioNetGen - Biological Network Generator
http://vcell.org/bionetgen
"Modeling and simulation tool. Predicts signal transduction model, based on PPIs. In addition, also provides option to define user interface parameters for proteins. Visualization of simulation results. "
"Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics. 2004 Nov 22;20(17):3289-91. Epub 2004 Jun 24. PubMed PMID: 15217809."
2004
100
BioPD - Bioactive Polypeptide Database
http://biopd.bjmu.edu.cn
"A resource that provides PPIs for the bioactive peptides. BioPD consists of six parts: PROTEIN, GENE, DISEASE, LINKS, INTERACTION, and REFERENCE."
"Shi L, Zhang Q, Rui W, Lu M, Jing X, Shang T, Tang J. BioPD: a web-based information center for bioactive peptides. Regul Pept. 2004 Aug 15;120(1-3):1-3. PubMed PMID: 15177914."
2004
100
BIOVERSE
http://bioverse.compbio.washington.edu
A database of experimentally-derived protein-protein interactions compiled from several sources. Predicted interaction partners are listed under the 'Function-Context'.
"McDermott J, Samudrala R. Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res. 2003 Jul 1;31(13):3736-7. PubMed PMID: 12824406; PubMed Central PMCID: PMC168957."
2003
100
BIOZON
http://www.biozon.org
"Unified resource on DNA sequences, proteins, complexes and cellular pathways. Analysis of proteins and their biological relationships including PPIs."
"Birkland A, Yona G. BIOZON: a hub of heterogeneous biological data. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D235-42. PubMed PMID: 16381854; PubMed Central PMCID: PMC1347515."
2006
100
BISC - BInary SubComplex
http://bisc.cse.ucsc.edu
"A database linking up the two communities: structural biology and functional genomics researchers. It offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces."
"Juettemann T, Gerloff DL. BISC: binary subcomplexes in proteins database. Nucleic Acids Res. 2011 Jan;39(Database issue):D705-11. Epub 2010 Nov 16. PubMed PMID: 21081561; PubMed Central PMCID: PMC3013763."
2010
100
BisKit
http://biskit.pasteur.fr
"A database for identifying protein-protein complexes, and docking."
"Grunberg R, Nilges M, Leckner J. Biskit--a software platform for structural bioinformatics. Bioinformatics. 2007 Mar 15;23(6):769-70. Epub 2007 Jan 18. PubMed PMID: 17237072."
2007
100
BisoGenet
http://bio.cigb.edu.cu/bisogenet
"Visualization and analysis of biomolecular relationships including PPIs for a given set of genes. Integrates PPI data from major resources like DIP, BIND & HPRD."
"Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R. BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics. 2010 Feb 17;11:91. PubMed PMID: 20163717."
2010
100
bZIPDB - Basic region-leucine zipper database
http://biosoft.kaist.ac.kr/bzipdb
"A repository of detailed regulatory information for human basic region-leucine zipper (bZIP) Transcription Factor (TF) proteins that is collected and processed from the literature. The database contains information on protein interaction data between bZIP TFs and other cellular proteins, along with other types of interactions, bZIP TF-target gene relationships, the cellular network of bZIP TFs in particular cell lines, and gene information and ontology."
"Ryu T, Jung J, Lee S, Nam HJ, Hong SW, Yoo JW, Lee DK, Lee D. bZIPDB: a database of regulatory information for human bZIP transcription factors. BMC Genomics. 2007 May 30;8:136. PubMed PMID: 17535445; PubMed Central PMCID: PMC1891292."
2007
100
CancerResource
http://bioinf-data.charite.de/cancerresource
A comprehensive knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data. It also has information on PPIs collected from consensusPathDB database.
"Ahmed J, Meinel T, Dunkel M, Murgueitio MS, Adams R, Blasse C, Eckert A, Preissner S, Preissner R. CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. Nucleic Acids Res. 2011 Jan;39(Database issue):D960-7. Epub 2010 Oct 15. PubMed PMID: 20952398; PubMed Central PMCID: PMC3013779."
2010
100
CANDID - A candidate gene identification program
https://dsgweb.wustl.edu/hutz/candid.html
A gene prioritization algorithm that includes PPI data too.
"Hutz JE, Kraja AT, McLeod HL, Province MA. CANDID: a flexible method for prioritizing candidate genes for complex human traits. Genet Epidemiol. 2008 Dec;32(8):779-90. Erratum in: Genet Epidemiol. 2008 Dec;32(8):816. PubMed PMID: 18613097."
2008
100
CAPPI - Conserved Ancestral Protein-Protein Interactions
http://bioputer.mimuw.edu.pl/papers/cappi
"A framework for protein network alignment, based on reconstruction of an ancestral PPI network. The reconstruction algorithm is built upon a proposed model of protein network evolution, which takes into account phylogenetic history of the proteins and the evolution of their interactions."
"Dutkowski J, Tiuryn J. Identification of functional modules from conserved ancestral protein-protein interactions. Bioinformatics. 2007 Jul 1;23(13):i149-58. PubMed PMID: 17646291."
2007
100
CBioC - Collaborative Bio Curation
http://cbioc.eas.asu.edu
A platform that automatically extracts PPIs for a given PMID. Also integrates data from other PPI databases.
"Baral C, Gonzalez G, Gitter A, Teegarden C, Zeigler A, Joshi-Tope G. CBioC: beyond a prototype for collaborative annotation of molecular interactions from the literature. Comput Syst Bioinformatics Conf. 2007;6:381-4. PubMed PMID: 17951840."
2007
100
CEBS - Chemical effects in biological systems
http://cebs.niehs.nih.gov/cebsdownload
"A knowledge base, being developed to house data from multiple complex data streams that would help in understanding the biological effects of environmental stressors. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and PPI analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics)."
"Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. EHP Toxicogenomics. 2003 Jan;111(1T):15-28. PubMed PMID: 12735106."
2003
100
Cell Interaction Knowledgebase
http://cell-interaction.bii.a-star.edu.sg
A resource tha provides interactions related to innate immunity pathway. Currently has data for mouse and human species.
"Chen S, Chinnaswamy A, Biswas SK, Goryachev AB, Yap CK, Lam KY, Tay CP, Low HS, Pokhilko A, Da-Jun T, Mishra SK. Cell interaction knowledgebase: an online database for innate immune cells, cytokines and chemokines. In Silico Biol. 2007;7(6):569-74. PubMed PMID: 18467769."
2007
100
CellCircuits
http://cellcircuits.org
"A database of molecular network models. It identifies functional subnetworks, based on expression or phenotypic data, internal structure or conservation across species. Can be searched by protein/gene names and Gene Ontology terms."
"Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan;35(Database issue):D538-45. Epub 2006 Nov 29. PubMed PMID: 17135207; PubMed Central PMCID: PMC1751555."
2006
100
CentrosomeDB - centrosomal proteins database
http://centrosome.dacya.ucm.es
"A database that contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Genes have been considered as centrosomal on the basis of different kinds of evidences including high-throughput proteomics assays, annotations in public databases and orthology relationships to centrosomal genes in closely related species. The PPI information for these genes have been compiled from HPRD."
"Nogales-Cadenas R, Abascal F, Díez-Pérez J, Carazo JM, Pascual-Montano A. CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Res. 2009 Jan;37(Database issue):D175-80. Epub 2008 Oct 29. PubMed PMID: 18971254; PubMed Central PMCID: PMC2686521."
2008
100
ChemProt
http://www.cbs.dtu.dk/services/ChemProt
"A disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated PPIs. The PPI network layer allows for studying disease and tissue specificity through each protein complex."
"Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI. ChemProt: a disease chemical biology database. Nucleic Acids Res. 2011 Jan;39(Database issue):D367-72. Epub 2010 Oct 8. PubMed PMID: 20935044; PubMed Central PMCID: PMC3013776."
2010
100
Chilibot
http://www.chilibot.net
"A specialized search software for the PubMed literature and is designed for identifying relationships between genes, proteins, or any keywords that the user might be interested. It can also process large number of terms/genes (e.g. microarray results). The relationships are summarized into graph, with links to sentences describing the relationships, as well as the terms themselves. "
"Chen H, Sharp BM. Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics. 2004 Oct 8;5:147. PubMed PMID: 15473905; PubMed Central PMCID: PMC528731."
2004
100
CIPHER - Correlating protein interaction network and phenotype network to predict disease genes
http://bioinfo.au.tsinghua.edu.cn/cipher
"A tool to predict and prioritize disease genes, by integrating protein interaction network and phenotype network. The method is applicable to genetically uncharacterized phenotypes, effective in the genome-wide scan of disease genes, and also extendable to explore gene cooperativity in complex diseases. The website has two versions of the predicted genetic landscape of human disease. One is predicted using protein interaction network from HPRD and the other is predicted on an extended network combining several high quality protein interaction databases. The results based on HPRD network may be more reliable, while the one based on the extended network may be more powerful in discovering novel disease genes."
"Wu X, Jiang R, Zhang MQ, Li S. Network-based global inference of human disease genes. Mol Syst Biol. 2008;4:189. Epub 2008 May 6. PubMed PMID: 18463613; PubMed Central PMCID: PMC2424293."
2008
100
ClusFCM
http://www.egr.vcu.edu/cs/dmb/ClusFCM
"An algorithm for predicting protein functions using protein homologies and protein interactions. It combines techniques of clustering and ""fuzzy cognitive maps"" for prediction of protein functions."
"Nguyen C, Mannino M, Gardiner K, Cios KJ. ClusFCM: an algorithm for predicting protein functions using homologies and protein interactions. J Bioinform Comput Biol. 2008 Feb;6(1):203-22. PubMed PMID: 18324753."
2008
100
ClusPro
http://structure.bu.edu/content/our-servers
A docking and discrimination method for the prediction of protein complexes.
"Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 2004 Jan 1;20(1):45-50. PubMed PMID: 14693807."
2004
100
COFECO - Composite Function Annotation Enriched by Protein Complex Data
http://piech.kaist.ac.kr/cofeco
"A tool for a composite annotation of protein complexes, KEGG pathways, and Gene Ontology (GO) terms within a class of genes and their orthologs. It also provides a web-based GO hierarchical viewer and KEGG pathway viewer where the enrichment results can be summarized and further explored."
"Sun CH, Kim MS, Han Y, Yi GS. COFECO: composite function annotation enriched by protein complex data. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W350-5. Epub 2009 May 8. PubMed PMID: 19429688; PubMed Central PMCID: PMC2703949."
2009
100
ConsensusPathDB
http://cpdb.molgen.mpg.de
"A meta-database that integrates functional interaction networks including complex, protein-protein, metabolic, signaling and gene regulatory interaction networks. Data originate from many public resources for functional interactions and interactions that have been curated from literature. Additionally, biochemical pathways have been imported from several databases for use in pathway analyses. Currently data available for human, yeast and mouse."
"Kamburov A, Wierling C, Lehrach H, Herwig R. ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D623-8. Epub 2008 Oct 21. PubMed PMID: 18940869; PubMed Central PMCID: PMC2686562."
2008
100
cons-PPISP - consensus Protein-Protein Interaction Site Predictor
http://pipe.scs.fsu.edu/ppisp.html
"A consensus neural network method for predicting protein-protein interaction sites. Given the structure of a protein, it will predict the residues that will likely form the binding site for another protein."
"Chen H, Zhou HX. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins. 2005 Oct 1;61(1):21-35. PubMed PMID: 16080151."
2005
100
Core
http://alse.cs.hku.hk/complexes
An open source program for predicting protein complexes from the PPI network by identifying their cores and attachments separately.
"Leung HC, Xiang Q, Yiu SM, Chin FY. Predicting protein complexes from PPI data: a core-attachment approach. J Comput Biol. 2009 Feb;16(2):133-44. PubMed PMID: 19193141."
2009
100
CORNET - CORrelation NETworks
https://bioinformatics.psb.ugent.be/cornet
"A data mining tool to analyze transcriptome, protein interactome, and localization data and functional information on Arabidopsis. It consists of two flexible and versatile tools, namely the co-expression tool and the PPI tool. The protein-protein interaction tool searches experimentally and computationally identified PPIs from various interaction databases."
"De Bodt S, Carvajal D, Hollunder J, Van den Cruyce J, Movahedi S, Inzé D. CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 2010 Mar;152(3):1167-79. Epub 2010 Jan 6. PubMed PMID: 20053712; PubMed Central PMCID: PMC2832254."
2010
100
CORUM - comprehensive resource of mammalian protein complexes
http://mips.helmholtz-muenchen.de/genre/proj/corum
"A resource that provides manually annotated protein complexes for mammalian organisms. Provides protein complex function, localization, subunit composition. Provides protein complexes for a biological processes, disease, etc."
"Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2008 Jan;36(Database issue):D646-50. Epub 2007 Oct 26. PubMed PMID: 17965090; PubMed Central PMCID:PMC2238909."
2007
100
CPLA - Compendium of Protein Lysine Acetylation
http://cpla.biocuckoo.org
"A manually curated database for lysine acetylated substrates with their sites. The database also provides Gene Ontology and InterPro annotations, and PPIs collected from various PPI databases."
"Liu Z, Cao J, Gao X, Zhou Y, Wen L, Yang X, Yao X, Ren J, Xue Y. CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res. 2011 Jan;39(Database issue):D1029-34. Epub 2010 Nov 8. PubMed PMID: 21059677; PubMed Central PMCID: PMC3013790."
2010
100
CYC2008 - Yeast protein complexes
http://wodaklab.org/cyc2008
A database of curated yeast protein complexes. It contains manually curated heteromeric protein complexes reliably backed by small-scale experiments reported in the current literature and high-throughput complexes annotated with current literature evidence.
"Pu S, Wong J, Turner B, Cho E, Wodak SJ. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009 Feb;37(3):825-31. Epub 2008 Dec 18. PubMed PMID: 19095691; PubMed Central PMCID: PMC2647312."
2008
100
Cytoprophet
http://cytoprophet.cse.nd.edu
A software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape. It implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include Maximum Likelihood Estimation (MLE) using Expectation Maximization (EM); the set cover approach Maximum Specificity Set Cover (MSSC) and the Sum-Product Algorithm (SPA).
"Morcos F, Lamanna C, Sikora M, Izaguirre J. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. Bioinformatics. 2008 Oct 1;24(19):2265-6. Epub 2008 Jul 24. PubMed PMID: 18653520."
2008
100
Cytoscape
http://www.cytoscape.org
"An open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases."
"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498-504. PubMed PMID: 14597658; PubMed Central PMCID: PMC403769."
2003
100
DADA - Degree-Aware Disease Gene Prioritization
http://compbio.case.edu/dada
A suite used for prioritizing candidate diseases genes based on the proximity of candidate genes with disease associated genes using PPI networks.
"Erten S, Bebek G, Ewing RM, Koyutürk M. DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min. 2011 Jun 24;4:19. PubMed PMID: 21699738; PubMed Central PMCID: PMC3143097."
2011
100
DAPID - Domain Annotated Protein-protein Interaction Database
http://gemdock.life.nctu.edu.tw/dapid
"A database of domain annotated protein interactions inferred from three-dimensional (3D) interacting domains of protein complexes in the Protein Data Bank. The DAPID data model allows users to visualize 3D interacting domains, contact residues, and molecular details of any predicted PPIs."
"Chen YC, Chen HC, Yang JM. DAPID: a 3D-domain annotated protein-protein interaction database. Genome Inform. 2006;17(2):206-15. PubMed PMID: 17503393."
2006
100
DASMI - Distributed Annotation System for Molecular Interactions
http://www.dasmi.de
"A system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization."
"Blankenburg H, Finn RD, Prlic A, Jenkinson AM, Ramirez F, Emig D, Schelhorn SE, Buch J, Lengauer T, Albrecht M. DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics. 2009 May 15;25(10):1321-8. PubMed PMID: 19420069; PubMed Central PMCID: PMC2677739."
2009
100
DASMIweb
http://www.dasmiweb.de
A web-server for the dynamic retrieval and sharing of molecular interaction datasets. It allows the user to integrate and qualitatively assess interaction data from multiple external resources with minimal effort. It also integrates confidence measures like functional similarity scores to assess individual interactions. It supports the inclusion of own interaction data. The retrieved results can be exported in different file formats like MITAB or SIF.
"Blankenburg H, Ramírez F, Büch J, Albrecht M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W122-8. Epub 2009 Jun 5. PubMed PMID: 19502495; PubMed Central PMCID: PMC2703953."
2009
100
DBMLoc
http://www.bioinfo.tsinghua.edu.cn/DBMLoc/index.htm
"A database of proteins with multiple subcellular localizations, collected from primary protein databases, specific subcellular localization databases and literature texts. All the protein entries are cross-referenced to Gene Ontology annotations and SwissProt, and PPIs are also annotated."
"Zhang S, Xia X, Shen J, Zhou Y, Sun Z. DBMLoc: a Database of proteins with multiple subcellular localizations. BMC Bioinformatics. 2008 Feb 28;9:127. PubMed PMID: 18304364; PubMed Central PMCID: PMC2292141."
2008
100
Death Domain database
http://www.deathdomain.org
A manually curated PPI database for the death domain superfamily proteins.
"Kwon D, Yoon JH, Shin SY, Jang TH, Kim HG, So I, Jeon JH, Ho Park H. A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. Nucleic Acids Res. 2011 Dec 1. [Epub ahead of print] PubMed PMID: 22135292."
2011
100
DEGAS - DysrEgulated Gene set Analysis via Subnetworks
http://acgt.cs.tau.ac.il/matisse/#degasref
"A method for analysis of clinical gene expression samples in the context of interaction networks (obtained from several interaction databases). Given a set of expression profiles labeled as cases and another set of controls, DEGAS aims to detect subnetworks in which multiple genes are dysregulated in the cases, while allowing for distinct affected gene sets in each case profile. The subnetworks identified by DEGAS can provide a signature of the disease potentially useful for diagnosis, pinpoint possible pathways affected by the disease, and suggest targets for drug intervention."
"Ulitsky I, Krishnamurthy A, Karp RM, Shamir R. DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One. 2010 Oct 19;5(10):e13367. PubMed PMID: 20976054; PubMed Central PMCID: PMC2957424."
2010
100
DePIE - Designing Primers for Protein Interaction Experiments
http://biocore.unl.edu/primer/primerPI.html
"A web-based primer design tool used for protein interaction experiments. The program takes as input NCBI protein accession numbers and returns primer information including nucleotide sequences, thermodynamic melting temperature of the nucleotide sequences and the target positions."
"Lu G, Hallett M, Pollock S, Thomas D. DePIE: Designing Primers for Protein Interaction Experiments. Nucleic Acids Res. 2003 Jul 1;31(13):3755-7. PubMed PMID: 12824411; PubMed Central PMCID: PMC168983."
2003
100
DICS
http://mips.gsf.de/proj/dics
"A database of computationally predicted functional modules from the human PPI network (human PPI data are collected from the IntAct, BIND, MINT and HPRD databases). It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. It can be used for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context."
"Dietmann S, Georgii E, Antonov A, Tsuda K, Mewes HW. The DICS repository: module-assisted analysis of disease-related gene lists. Bioinformatics. 2009 Mar 15;25(6):830-1. Epub 2009 Jan 28. PubMed PMID: 19176557."
2009
100
DIG - Duke Integrated Genomics
http://dig.cagp.duke.edu
"A database and information discovery system designed to facilitate the process of gene annotation and the discovery of functional context. It provides a framework for integrating and visualizing gene expression, protein interaction and literature-based interaction networks."
"Delong M, Yao G, Wang Q, Dobra A, Black EP, Chang JT, Bild A, West M, Nevins JR, Dressman H. DIG--a system for gene annotation and functional discovery. Bioinformatics. 2005 Jul 1;21(13):2957-9. Epub 2005 May 3. PubMed PMID: 15870167."
2005
100
DIMA - Domain Interaction Map
http://mips.gsf.de/genre/proj/dima
"A web-resource which integrates data sources describing or predicting links among conserved protein domains resulting in a domain interaction map. The user can search for individual domains, navigate through the network and visualize subnets."
"Pagel P, Oesterheld M, Stümpflen V, Frishman D. The DIMA web resource--exploring the protein domain network. Bioinformatics. 2006 Apr 15;22(8):997-8. Epub 2006 Feb 15. PubMed PMID: 16481337."
2006
100
DIP - Database of Interacting Proteins
http://dip.doe-mbi.ucla.edu/dip
A database that provides PPIs of experimental importance. Provides interactions for a specific protein family. Provides the interactions along with the complexes involved. Provides option to BLAST a given protein sequence. Provide PPIs for a given PMID of article.
"Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res. 2000 Jan 1;28(1):289-91. PubMed PMID: 10592249; PubMed Central PMCID: PMC102387."
2000
100
DIPOS - Database of Interacting Proteins in Oryza sativa
http://csb.shu.edu.cn/dipos
"A database that provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain based methods. Each interaction is assigned a confidence score which further enables biologists to sort out the important proteins."
"Sapkota A, Liu X, Zhao XM, Cao Y, Liu J, Liu ZP, Chen L. DIPOS: database of interacting proteins in Oryza sativa. Mol Biosyst. 2011 Sep 1;7(9):2615-21. Epub 2011 Jun 29. PubMed PMID: 21713282."
2011
100
dmGWAS
http://bioinfo.mc.vanderbilt.edu/dmGWAS.html
A dense module searching method to identify candidate sub-networks or genes for complex diseases by integrating the association signal from GWAS (genome-wide association studies) datasets into the human PPI network.
"Jia P, Zheng S, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics. 2011 Jan 1;27(1):95-102. Epub 2010 Nov 2. PubMed PMID: 21045073; PubMed Central PMCID: PMC3008643."
2010
100
DomainGraph
http://www.domaingraph.de
"A software platform for the analysis and visualization of molecular interaction networks. The main functionality of the DomainGraph plugin is the visual analysis of the effects of alternative splicing on genes, protein isoforms, molecular interactions, pathways and miRNA binding sites."
"Emig D, Cline MS, Lengauer T, Albrecht M. Integrating expression data with domain interaction networks. Bioinformatics. 2008 Nov 1;24(21):2546-8. Epub 2008 Aug 18. PubMed PMID: 18710874; PubMed Central PMCID: PMC2572699."
2008
100
DOMINE - Database of Protein Domain Interactions
http://domine.utdallas.edu
"A comprehensive collection of known and predicted domain-domain interactions. It contains interactions inferred from PDB entries, and those that are predicted by different computational approaches using Pfam domain definitions."
"Raghavachari B, Tasneem A, Przytycka TM, Jothi R. DOMINE: a database of protein domain interactions. Nucleic Acids Res. 2008 Jan;36(Database issue):D656-61. Epub 2007 Oct 2. PubMed PMID: 17913741; PubMed Central PMCID: PMC2238965."
2007
100
DOMINO - domain peptide interactions
http://mint.bio.uniroma2.it/domino
Curated database of domain-peptide interactions. Interactions to a specific experimental evidence can be restricted. Provides option to curate data for the database.
"Ceol A, Chatr-aryamontri A, Santonico E, Sacco R, Castagnoli L, Cesareni G. DOMINO: a database of domain-peptide interactions. Nucleic Acids Res. 2007 Jan;35(Database issue):D557-60. Epub 2006 Nov 29. PubMed PMID: 17135199; PubMed Central PMCID: PMC1751533."
2006
100
DOMMINO - Database Of MacroMolecular INteractiOns
http://dommino.org
"A comprehensive database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."
"Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. DOMMINO: a database of macromolecular interactions. Nucleic Acids Res. 2011 Dec 1. [Epub ahead of print] PubMed PMID: 22135305."
2011
100
Dr. PIAS - Druggable Protein-protein Interaction Assessment System
http://asp.gridasp.net/drpias
"A system for assessing the druggability of PPIs. It has various types of information on tertiary structures, drugs and chemicals, and biological function associated with PPIs retrieved from public databases. By utilizing this information, Dr. PIAS assesses the druggability of PPIs with a supervised machine-learning method, support vector machine."
"Sugaya N, Furuya T. Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. BMC Bioinformatics. 2011 Feb 9;12:50. PubMed PMID: 21303559."
2011
100
DroID - Drosophila Interactions Database
http://droidb.org
"A comprehensive public resource for Drosophila gene and protein interactions. It contains genetic interactions and experimentally detected PPIs curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. In addition to protein-protein and genetic interactions, the database also includes transcription factor-gene and regulatory RNA-gene interactions."
"Yu J, Pacifico S, Liu G, Finley RL Jr. DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics. 2008 Oct 7;9:461. PubMed PMID: 18840285; PubMed Central PMCID: PMC2572628."
2008
100
DRYGIN - Data Repository of Yeast Genetic Interactions
http://drygin.ccbr.utoronto.ca
"A database of quantitative genetic interactions of yeast derived from the Synthetic Genetic Array (SGA) double-mutant arrays. In addition to genetic interactions, the database also integrates other data sources, in order to associate the genetic interactions with pathway information, protein complexes, other binary genetic and physical interactions, and Gene Ontology functional annotation."
"Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub 2009 Oct 30. PubMed PMID: 19880385; PubMed Central PMCID: PMC2808960."
2009
100
EchoBASE - an integrated post-genomic database of E.coli
http://www.ecoli-york.org
"A database that curates new experimental and bioinformatics information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. Currently, data is manually curated from published experimental research and sorted into one of the following 'types' of experiments: proteomics; microarray; transcript level; genetics; biochemistry; bioinformatics, PPIs and structure."
"Misra RV, Horler RS, Reindl W, Goryanin II, Thomas GH. EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D329-33. PubMed PMID: 15608209; PubMed Central PMCID: PMC539982."
2005
100
ECID - E. coli Interaction Database
http://ecid.bioinfo.cnio.es
"A database related to PPIs in E. coli. It integrates functional interactions from the following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information), KEGG (metabolic pathways) and MINT (protein interactions). It also contains information on protein complexes from the two published high throughput pull down experiments carried out in E. coli, and potential interactions directly extracted from the literature using the web-services associated to the iHOP text-mining system. In addition, the database incorporates results from two protein interaction prediction methods based on genomic information (Phylogenetic Profiles and Gene Neighborhoods) and three methods based on analysis of the potential co-evolution of the corresponding protein families (Mirror Tree, In Silico 2 Hybrid and Context Mirror). ECID provides each predicted pair a confidence score that reflects the reliability of the functional interaction between those two proteins."
"Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D. EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res. 2009 Jan;37(Database issue):D629-35. Epub 2008 Nov 12. PubMed PMID: 19004873; PubMed Central PMCID: PMC2686479."
2008
100
EDGEdb - C. elegans differential gene expression database
http://edgedb.umassmed.edu
A database that provides protein-DNA -and protein-protein interaction for C. elegans transcription factors.
"Barrasa MI, Vaglio P, Cavasino F, Jacotot L, Walhout AJ. EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics. 2007 Jan 18;8:21. PubMed PMID: 17233892; PubMed Central PMCID: PMC1790901."
2007
100
Endeavour
http://www.esat.kuleuven.be/endeavourweb
"A tool for the prioritization of candidates genes, based on a set of training genes. It is made up of three stages: training, scoring and fusion. In the first stage, information about the training genes (genes already known to play a role in the process under study) are retrieved from numerous data sources in order to build models. The information includes functional annotations, PPIs, regulatory information, expression data, sequence based data and literature mining data. In the second stage, the models are then used to score the candidate genes and to rank them according to their scores. In the last stage, the rankings per data source are fused into a global ranking using order statistics. It currently supports human, mouse, rat, fruit fly and worm species."
"Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006 May;24(5):537-44. Erratum in: Nat Biotechnol. 2006 Jun;24(6):719. PubMed PMID: 16680138."
2006
100
ePlant
http://bar.utoronto.ca/eplant
"A suite of open-source web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer."
"Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ. ePlant and the 3D data display initiative: integrative systems biology on the world wide web. PLoS One. 2011 Jan 10;6(1):e15237. PubMed PMID: 21249219; PubMed Central PMCID: PMC3018417."
2011
100
Faspad - Fast signaling pathway detection
http://theinf1.informatik.uni-jena.de/faspad
"A tool that detects candidates for linear signaling pathways in protein interaction networks based on a published approach (Scott et al. Journal of Computational Biology, 2006)."
"Hüffner F, Wernicke S, Zichner T. Faspad: fast signaling pathway detection. Bioinformatics. 2007 Jul 1;23(13):1708-9. Epub 2007 Apr 26. PubMed PMID: 17463016."
2007
100
Fly-DPI - Drosophila melanogaster Database of Protein Interactomes
http://flydpi.nhri.org.tw
"A system for predicting PPIs of Drosophila melanogaster, based on known PPI data, integrated with complete protein annotation information from major databases. It is designed to explore in-depth potential protein interaction relationships, and provides reliability estimates for PPIs for both experimental and inferred interaction, which can be used to build a protein interaction network and predict novel interactions."
"Lin CY, Chen SH, Cho CS, Chen CL, Lin FK, Lin CH, Chen PY, Lo CZ, Hsiung CA. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S18. PubMed PMID: 17254302; PubMed Central PMCID: PMC1764474."
2006
100
FlyNets
http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page. ?
"A database of molecular interactions in the fly Drosophila melanogaster. It is composed of two parts, as follows. (i) FlyNets-base is a specialized database which focuses on molecular interactions involved in Drosophila development. The FlyNets database achieves a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. (ii) FlyNets-list is a very simple and more general databank, the long-term goal of which is to report on any published molecular interaction occuring in the fly, giving direct web access to corresponding links in Medline and in FlyBase."
"Mohr E, Horn F, Janody F, Sanchez C, Pillet V, Bellon B, Röder L, Jacq B. FlyNets and GIF-DB, two internet databases for molecular interactions in Drosophila melanogaster. Nucleic Acids Res. 1998 Jan 1;26(1):89-93. PubMed PMID: 9399807; PubMed Central PMCID: PMC147170."
1998
100
FPPI - F. graminearum protein-protein interaction
http://csb.shu.edu.cn/fppi
"A database that provides comprehensive information on PPIs of Fussarium graminearum, predicted based on both interologs from several PPI databases of seven species and domain-domain interactions experimentally determined based on protein structures. The predicted interactome covers about 52% of the whole F. graminearum proteome, and each interaction is assigned a score as the confidence for the predicted PPI. Furthermore, this database contains various different functional information for F. graminearum genes. In summary, FPPI is a rich source of information for system-level understanding of gene functions and biological processes in F. graminearum."
"Zhao XM, Zhang XW, Tang WH, Chen L. FPPI: Fusarium graminearum protein-protein interaction database. J Proteome Res. 2009 Oct;8(10):4714-21. PubMed PMID: 19673500."
2009
100
Friend
http://mozart.bio.neu.edu/friend
"A bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities, such as structure visualization, sequence alignment and simple phylogeny analysis, along with a number of extended features including structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions and protein super-families."
"Abyzov A, Errami M, Leslin CM, Ilyin VA. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15;21(18):3677-8. Epub 2005 Aug 2. PubMed PMID: 16076889."
2005
100
FunCoup - Networks of functional coupling
http://FunCoup.sbc.su.se
"A statistical framework for finding functional coupling (FC) between proteins, by Bayesian data integration. It transfers information from model organisms via orthologs found by InParanoid program. It also includes predicted global interactomes for H. sapiens, M. musculus, R. norvegicus, C. intestinalis, D. melanogaster, C. elegans, S. cerevisiae, A. thaliana. Along with the physical interactions, user can also query for complexes, metabolic and signalink links between the input genes/proteins."
"Alexeyenko A, Sonnhammer EL. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res. 2009 Jun;19(6):1107-16. Epub 2009 Feb 25. PubMed PMID: 19246318; PubMed Central PMCID: PMC2694487."
2009
100
g:Profiler
http://biit.cs.ut.ee/gprofiler
"A collection of web tools for functional analysis of gene lists from high-throughput genomics. g:GOSt and g:Cocoa combine comprehensive methods for interpreting gene lists in the context of biomedical ontologies, pathways, transcription factor and microRNA regulatory motifs and PPIs. Additional tools, namely g:Convert, g:Sorter and g:Orth provide numerous ways for further analysis and interpretation. Currently it supports 80 species, including mammals, plants, fungi, insects, etc. from Ensembl and Ensembl Genomes."
"Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200. Epub 2007 May 3. PubMed PMID: 17478515; PubMed Central PMCID: PMC1933153."
2007
100
Gaggle
http://gaggle.systemsbiology.net
"An open-source Java software environment, which has integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). It enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and PubMed abstracts (STRING web resource)."
"Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. 2006 Mar 28;7:176. PubMed PMID: 16569235; PubMed Central PMCID: PMC1464137."
2006
100
GAIA - Gram-bAsed Interaction Analysis
http://www.oicr.on.ca/research/ouellette/gaia
"An approach to predict Domain-Domain Interactions (DDIs) in yeast. It extracts peptide segments that are composed of fixed length of continuous amino acids, called n-grams (where n is the number of amino acids), from the annotated domain and DDI data set in Saccharomyces cerevisiae (budding yeast) and identifies a list of n-grams that may contribute to DDIs and PPIs based on the frequencies of their appearance. It also reports the coordinate position of gram pairs on each interacting domain pair."
"Zhang KX, Ouellette BF. GAIA: a gram-based interaction analysis tool--an approach for identifying interacting domains in yeast. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S60. PubMed PMID: 19208164; PubMed Central PMCID: PMC2648738."
2009
100
GARNET - Gene Annotation Relationship NEtwork Tools
http://garnet.isysbio.org
"An integrative platform for gene set analysis, which includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. A variety of annotation data have been integrated, that include the Gene Ontology, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks such as, pathways, transcription and microRNA regulations, and PPIs are also included."
"Rho K, Kim B, Jang Y, Lee S, Bae T, Seo J, Seo C, Lee J, Kang H, Yu U, Kim S, Lee S, Kim WK. GARNET--gene set analysis with exploration of annotation relations. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S25. PubMed PMID: 21342555; PubMed Central PMCID: PMC3044280."
2011
100
GenAge
http://genomics.senescence.info
A manually curated database of genes related to ageing. The database includes genes directly related to ageing in humans and the best candidate genes obtained from model organisms. It provides other supporting information including PPIs for these genes.
"de Magalhães JP, Toussaint O. GenAge: a genomic and proteomic network map of human ageing. FEBS Lett. 2004 Jul 30;571(1-3):243-7. PubMed PMID: 15280050."
2004
100
Gene3D - Structure Assigned to Genomes
http://gene3d.biochem.ucl.ac.uk
"A resource that provides accurate structural domain family assignments. A variety of protein annotation resources, including PPI data, Gene Ontology functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data also have been included to enhance the investigation."
"Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. 2003 Jan 1;31(1):469-73. PubMed PMID: 12520054; PubMed Central PMCID: PMC165498."
2003
100
GeneDistiller
http://www.genedistiller.org
"A web-based application that integrates gene related information from various resources. Information such as gene-phenotype associations, gene expression patterns and protein-protein interactions is integrated into a central database. The required information for the genes within a candidate interval or for single genes can be selected and displayed. Genes can also interactively be filtered, sorted and prioritized according to the criteria derived from the background knowledge and preconception of the disease under study."
"Seelow D, Schwarz JM, Schuelke M. GeneDistiller--distilling candidate genes from linkage intervals. PLoS One. 2008;3(12):e3874. Epub 2008 Dec 5. PubMed PMID: 19057649; PubMed Central PMCID: PMC2587712."
2008
100
GenePro
http://genepro.ccb.sickkids.ca
A Cytoscape plugin featuring a set of versatile tools that facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules.
"Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ. GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks. Bioinformatics. 2006 Sep 1;22(17):2178-9. PubMed PMID: 16921162."
2006
100
GeneRanker
http://www.generanker.org
"An online system that allows researchers to obtain a ranked list of genes potentially related to a disease or biological process by combining gene-disease associations with PPIs extracted from the literature, using computational analysis of the protein network topology to more accurately rank the predicted associations."
"Gonzalez G, Uribe JC, Armstrong B, McDonough W, Berens ME. GeneRanker: An Online System for Predicting Gene-Disease Associations for Translational Research. Summit on Translat Bioinforma. 2008 Mar 1;2008:26-30. PubMed PMID: 21347122; PubMed Central PMCID: PMC3041521."
2008
100
Genes2Networks
http://actin.pharm.mssm.edu/genes2networks
A tool for creating sub-networks from lists of mammalian genes or proteins by connecting these genes or proteins using known PPIs. Currently it integrates the content of ten mammalian interaction network datasets.
"Berger SI, Posner JM, Ma'ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics. 2007 Oct 4;8:372. PubMed PMID: 17916244; PubMed Central PMCID: PMC2082048."
2007
100
GeneWays
http://anya.igsb.anl.gov/Geneways
"A system for automatically extracting, analzying, visualizing and integrating molecular pathway data from the literature. The system focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. It is designed as an open platform, allowing researchers to query, review and critique the integrated information."
"Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb;37(1):43-53. PubMed PMID: 15016385."
2004
100
GEOMI
http://www.systemsbiology.org.au/downloads_geomi.html
"A three dimensional network visualization platform, that allows the coanalysis of PPI networks with proteomic parameters such as protein localization, abundance, physicochemical parameters, post-translational modifications, and Gene Ontology classification. The SBI version of GEOMI enables visualisation of PPI data in four-dimensions."
"Ho E, Webber R, Wilkins MR. Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J Proteome Res. 2008 Jan;7(1):104-12. Epub 2007 Nov 20. PubMed PMID: 18020406."
2007
100
GermOnline
www.germonline.org
"A cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It provides access to information produced with high-density oligonucleotide microarrays, genome-wide protein-DNA binding assays and PPI studies (from BioGRID and IntAct) in the context of Ensembl genome annotation."
"Primig M, Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Dickinson HG, Fellous M, Grootegoed JA, Hawley RS, Jégou B, Maro B, Nicolas A, Orr-Weaver T, Schedl T, Villeneuve A, Wolgemuth DJ, Yamamoto M,Zickler D, Lamb N, Esposito RE. GermOnline, a new cross-species community annotation database on germ-line development and gametogenesis. Nat Genet. 2003 Dec;35(4):291-2. PubMed PMID: 14647278."
2003
100
GIM - Gene Interaction Miner
http://www.cs.newcastle.edu.au/~mendes/softwareGIM.html
An automated tool for discovery of genetic networks and the availability of extensive contextual PPI information in the iHOP repository.
"Ikin A, Riveros C, Moscato P, Mendes A. The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis. Bioinformatics. 2010 Jan 15;26(2):283-4. Epub 2009 Dec 4. PubMed PMID: 19965878."
2009
100
go2ppi
http://acb.qfab.org/acb/go2ppi
"A predictor for PPIs based on Gene Ontology (GO) annotations. The predictor reads a list of protein identifiers with their corresponding GO annotations. It generates a list of protein pairs with a confidence value, which indicates whether two proteins are likely to interact or not."
"Maetschke SR, Simonsen M, Davis MJ, Ragan MA. Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinformatics. 2011 Nov 4. [Epub ahead of print] PubMed PMID: 22057159."
2011
100
GOAPhAR - Gene Ontology, Annotations and Pathways for Array Research
http://bioinformatics.kumc.edu/goaphar
"A web-based tool that gives information about gene identifiers with respect to their gene annotation, protein annotation, protein interactions, biological pathways, Gene Ontology associations. The data corresponding to each annotation type is collected from varoius sources. It also gives identifiers associated from different databases, presence of available microarray datasets, statistical validity of clusters of microarray data and description from affymetrix. The results displayed in a table can be downloaded in the text file."
"Mathur S, Visvanathan M, Svojanovsky S, Yoo B, Srinivas AB, Lushington GH, Smith PG. GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. Open Bioinforma J. 2009 Jan 1;3:26-30. PubMed PMID: 21132056; PubMed Central PMCID: PMC2995274."
2009
100
gpDB - a database of GPCRs, G-proteins, Effectors and their interactions
http://bioinformatics.biol.uoa.gr/gpDB
A resource for G-proteins and their interactions with G-protein Coupled Receptors (GPCRs) and effector molecules. Provides option to BLAST the input sequence.
"Theodoropoulou MC, Bagos PG, Spyropoulos IC, Hamodrakas SJ. gpDB: a database of GPCRs, G-proteins, effectors and their interactions. Bioinformatics. 2008 Jun 15;24(12):1471-2. Epub 2008 Apr 25. PubMed PMID: 18441001."
2008
100
GPS-Prot - A Browser for Protein Interaction Databases
http://www.gpsprot.org
"A web-based software tool that allows integration of different HIV interaction data types as well as inclusion of interactions between human proteins derived from publicly-available databases, including MINT, BioGRID and HPRD. It can group proteins into functional modules or protein complexes, generating more intuitive network representations and also allows for the uploading of user-generated data."
"Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics. 2011 Jul 22;12:298. PubMed PMID: 21777475."
2011
100
Graphle
http://sonorus.princeton.edu/graphle
"An interactive tool for exploration of biological network, available as online and downloadable versions. Finds both experimental and predicted relationships among the queried genes/proteins. Functional relationship networks are predicted by the bioPIXIE system for yeast, the HEFalMp system for humans, and a collection of microarray data integrated from GEO for E. coli."
"Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 2009 Dec 14;10:417. PubMed PMID: 20003429; PubMed Central PMCID: PMC2803856."
2009
100
GRIP - Gold Reference dataset constructor from Information on Protein complexes
http://rosalind.infj.ulst.ac.uk/GRIP
A web-based system that provides researchers with the functionality to create reference datasets for PPI prediction in Saccharomyces cerevisiae. It also provides an upload option whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in yeast.
"Browne F, Wang H, Zheng H, Azuaje F. GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction. Source Code Biol Med. 2009 Jan 26;4:2. PubMed PMID: 19171033; PubMed Central PMCID: PMC2636808."
2009
100
GRIPDB - G-protein coupled Receptor Interaction Partners DataBase
http://grip.cbrc.jp/GDB
"A database about G-protein Coupled Receptor (GPCRs) oligomerization. It provides, experimentally suggested information about GPCR oligomerization, experimentally suggested interface regions for GPCR oligomerization and predicted interface regions by bioinformatics methods."
"Nemoto W, Fukui K, Toh H. GRIPDB - G protein coupled Receptor Interaction Partners DataBase. J Recept Signal Transduct Res. 2011 Jun;31(3):199-205. Epub 2011 Mar 17. PubMed PMID: 21410407."
2011
100
GROMO - Genomic Resources of Magnaporthe oyzae
http://gromo.msubiotech.ac.in
"A specialized and comprehensive database for rice blast fungus Magnaporthe oyzae, with integrated information from several resources. It contains information on genomic sequence, mutants, gene expression, localization of proteins, obtained from various repositories. In addition, prediction of domains, pathways, PPIs, sumolyation sites and biochemical properties using computational analysis of protein sequences have also been included in the database."
"Thakur S, Jha S, Roy-Barman S, Chattoo B. Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus. BMC Genomics. 2009 Jul 15;10:316. PubMed PMID: 19604367; PubMed Central PMCID: PMC2721851."
2009
100
GWIDD - Genome Wide Docking Database
http://gwidd.bioinformatics.ku.edu
An integrated resource for structural studies of PPIs on genome-wide scale. It contains known PPIs and allows input of other sequences and structures to find interacting proteins and obtain the modeled 3D structures of their complexes. In includes variety of organisms ranging from viruses to plants and animals.
"Kundrotas PJ, Zhu Z, Vakser IA. GWIDD: Genome-wide protein docking database. Nucleic Acids Res. 2010 Jan;38(Database issue):D513-7. Epub 2009 Nov 9. PubMed PMID: 19900970; PubMed Central PMCID: PMC2808876."
2009
100
HAPPI - Human Annotated and Predicted Protein Interaction
http://bio.informatics.iupui.edu/HAPPI
"A database that was created by extracting and integrating publicly available interaction data from protein interaction databases, including HPRD, BIND, MINT, STRING, and OPHID. A unified scoring model was applied to give each PPI a measure of its reliability that can place each PPI at one of the five star rank levels from 1 to 5. It also provides hyperlinked information of genes, pathways, protein domains, protein structure displays, and sequence feature maps for interactive exploration of PPI data in the database."
"Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics. 2009 Jul 7;10 Suppl 1:S16. PubMed PMID: 19594875; PubMed Central PMCID: PMC2709259."
2009
100
HCCNet - Hepatocellular carcinoma network database
http://www.megabionet.org/hcc
"A compiled network of thousands of HepatoCellular Carcinoma (HCC) related genes indentified in different types and stages of samples. Also gives information on miRNAs related to HCC, PPIs and pathways for the HCC genes."
"He B, Qiu X, Li P, Wang L, Lv Q, Shi T. HCCNet: an integrated network database of hepatocellular carcinoma. Cell Res. 2010 Jun;20(6):732-4. Epub 2010 May 18. PubMed PMID: 20479783."
2010
100
HCPIN - Human Cancer Protein Interaction Network
http://nmr.cabm.rutgers.edu/hcpin
"A database of human proteins that participate in cancer-associated signaling pathways, and their PPIs. It integrates (embeds) pathway data with PPI data and provides protein structure-function annotations to inform cancer biology."
"Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, Montelione GT. Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics. 2008 Oct;7(10):2048-60. Epub 2008 May 18. PubMed PMID: 18487680; PubMed Central PMCID: PMC2559933."
2008
100
HCVpro - Hepatitis C Virus Protein Interaction Database
http://cbrc.kaust.edu.sa/hcvpro
"A database on hepatitis C virus-virus and virus-human protein interactions. It contains both manually verified literature and database curated interactions. Protein interactions databases employed for the curations were: BIND, VirusMINT and VirHostNet. Additionally, functional annotation data were obtained from publicly available annotation resources and published literature. It is further populated with information on hepatocellular carcinoma related genes that are mapped onto their encoded cellular proteins. The proteins in the database have been mapped onto Gene Ontologies, canonical pathways, OMIM and extensively cross-referenced to other essential annotations."
"Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A. HCVpro: Hepatitis C virus protein interaction database. Infect Genet Evol. 2011 Sep 9. [Epub ahead of print] PubMed PMID: 21930248."
2011
100
heinz - heavy induced subgraphs
http://www.mi.fu-berlin.de/w/LiSA/Heinz
A software that Identifyies functional modules in PPI networks. It computes provably optimal subnetworks in large protein interaction networks and also has a scoring function defined on the network nodes.
"Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics. 2008 Jul 1;24(13):i223-31. PubMed PMID: 18586718; PubMed Central PMCID: PMC2718639."
2008
100
H-InvDB - H-Invitational Database
http://www.h-invitational.jp
"An integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts that include gene structures, alternative splicing variants, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , PPIs and gene families/groups."
"Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene. 2005 Dec 30;364:99-107. Epub 2005 Sep 26. PubMed PMID: 16185827."
2005
100
HIPPIE - Human Integrated Protein-Protein Interaction rEference
http://cbdm.mdc-berlin.de/tools/hippie
A database that integrates interaction data from various source databases and studies that have not been fully covered by the other databases yet. HIPPIE assigns a confidence score to the interactions based on the amount and reliability of evidence supporting each interaction.
Not available
Not available
100
HitPredict - a database of high confidence protein-protein interactions
http://hintdb.hgc.jp/htp
"A resource of high confidence PPIs. The interactions from IntAct, BIOGRID and HPRD are combined, annotated and assigned a reliability score in order to identify a high confidence subset. The reliability score is calculated as the likelihood ratio using naive Bayesian networks combining sequence, structure and functional annotations of the interacting proteins. Currently the database has PPIs across 9 species."
"Patil A, Nakai K, Nakamura H. HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 2011 Jan;39(Database issue):D744-9. Epub 2010 Oct 14. PubMed PMID: 20947562; PubMed Central PMCID: PMC3013773."
2010
100
"HIV-1, human, protein interaction database"
www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions
"A catalog of all interactions between HIV-1 and human proteins curated from the published literature. The database has been designed track the following information for each PPI identified in the literature: RefSeq protein accession numbers, Entrez Gene identifiers, brief descriptions of the interactions, amino acid sequence of each interacting protein, searchable keywords for interactions and PMIDs of journal articles describing the interactions."
"Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res. 2009 Jan;37(Database issue):D417-22. Epub 2008 Oct 15. PubMed PMID: 18927109; PubMed Central PMCID: PMC2686594."
2008
100
Homeodomain
http://research.nhgri.nih.gov/homeodomain
"A curated collection of sequence, structure, PPIs, genomic, and functional information on the homeodomain family proteins. "
"Moreland RT, Ryan JF, Pan C, Baxevanis AD. The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family. Database (Oxford). 2009;2009:bap004. Epub 2009 Apr 17. PubMed PMID: 20157477; PubMed Central PMCID: PMC2790301."
2009
100
HomoMINT - an inferred human network
http://mint.bio.uniroma2.it/HomoMINT
"A database of inferred human protein interactions, based on orthology mapping of protein interactions discovered in model organisms. The orthology groups in HomoMINT are obtained by the reciprocal best hit method as implemented in the ""Inparanoid algorithm""."
"Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G. HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S21. PubMed PMID: 16351748; PubMed Central PMCID: PMC1866386."
2005
100
HomPPI - Protein-Protein Binding Site Predictor
http://homppi.cs.iastate.edu
"A class of sequence homology-based methods for predicting protein-protein interface residues. There are two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used to predict the interface residues of a query protein with a specific target protein."
"Xue LC, Dobbs D, Honavar V. HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics. 2011 Jun 17;12:244. PubMed PMID: 21682895; PubMed Central PMCID: PMC3213298."
2011
100
HPID - Human Protein Interaction Database
http://www.hpid.org
"A human protein interaction database that provides interaction information, pre-computed from existing structural and experimental data. It also predicts potential interactions between proteins submitted by users and provides a depository for new human protein interaction data from users. Two types of interaction are available from the pre-computed data: interactions at the protein superfamily level and those transferred from the interactions of yeast proteins."
"Han K, Park B, Kim H, Hong J, Park J. HPID: the Human Protein Interaction Database. Bioinformatics. 2004 Oct 12;20(15):2466-70. Epub 2004 Apr 29. PubMed PMID: 15117749."
2004
100
HPIDB - Host - Pathogen Interaction Database
http://agbase.msstate.edu/hpi/main.html
"A unified, comprehensive resource for host-pathogen PPIs. It integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a various options such as sequence, identifiers, symbol, taxonomy, publication, author, or interaction type. It can also be searched for homologous host-pathogen interactions. "
"Kumar R, Nanduri B. HPIDB--a unified resource for host-pathogen interactions. BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S16. PubMed PMID: 20946599; PubMed Central PMCID: PMC3026363."
2010
100
HPRD - Human Protein Reference Database
http://www.hprd.org
Curated database that provides protein related information including PPIs.
"Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct;13(10):2363-71. PubMed PMID: 14525934; PubMed Central PMCID: PMC403728."
2003
100
hPRINT - Human Predicted Protein Interactome
http://www.print-db.org
"A database on predicted physical and functional human PPIs. It is using a combination of random forest and Bayesian learning approaches in order to integrate various evidences (text mining, genetic relationships, evolutionary information, and domain profiles) for predicting PPIs and integrating those predictions with known information."
"Elefsinioti A, Saraç OS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. Large-scale De Novo Prediction of Physical Protein-Protein Association. Mol Cell Proteomics. 2011 Nov;10(11):M111.010629. Epub 2011 Aug 11. PubMed PMID: 21836163."
2011
100
Hubba - Hub Objects Analyzer
http://hub.iis.sinica.edu.tw/Hubba
"A web-based tool for exploring important nodes in an interactome network generated from specific small or large scale experimental methods based on graph theory. Six characteristic analysis algorithms, Degree, BottleNeck (BN), Edge Percolation Component (EPC), Subgraph Centrality (SC), Maximum Neighborhood Component (MNC), and the Density of Maximum Neighborhood Component (DMNC) are developed for exploring and identifying hubs/essential nodes from interactome networks."
"Lin CY, Chin CH, Wu HH, Chen SH, Ho CW, Ko MT. Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W438-43. Epub 2008 May 24. PubMed PMID: 18503085; PubMed Central PMCID: PMC2447731."
2008
100
HUGE ppi - A Database of protein-protein interactions between large proteins
http://www.kazusa.or.jp/huge/ppi
A database of PPIs of large proteins. The interactions were identified with the help of yeast two-hybrid screening using KIAA cDNA library.
"Nakayama M, Kikuno R, Ohara O. Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs. Genome Res. 2002 Nov;12(11):1773-84. PubMed PMID: 12421765; PubMed Central PMCID: PMC187542."
2002
100
Human Proteinpedia
http://www.humanproteinpedia.org
"A community portal for sharing and integration of human protein data. Data pertaining to post-translational modifications, PPIs, tissue expression etc., can be submitted to Human Proteinpedia. HPRD integrates the data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein."
"Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A. Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res. 2009 Jan;37(Database issue):D773-81. Epub 2008 Oct 23. PubMed PMID: 18948298; PubMed Central PMCID: PMC2686511."
2008
100
I2D (earlier OPHID) - Interologous Interaction Database
http://ophid.utoronto.ca
"An online database of known and predicted mammalian and eukaryotic PPIs. It includes data for S. cerevisiae, C. elegans, D. melonogaster, R. norvegicus, M. musculus, and H. sapiens"
"Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics. 2005 May 1;21(9):2076-82. Epub 2005 Jan 18. PubMed PMID: 15657099."
2005
100
Inter-Chain Beta-Sheets (ICBS) - A database of protein-protein interactions mediated by interchain beta-sheet formation
http://www.igb.uci.edu/servers/icbs
"A database that identifies and characterizes all interchain beta-sheet interactions within entries in PDB and the Protein Quaternary Structure server (PQS), of the Macromolecular Structure Database of the European Bioinformatics Institute."
"Dou Y, Baisnée PF, Pollastri G, Pécout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Bioinformatics. 2004 Nov 1;20(16):2767-77. Epub 2004 May 27. PubMed PMID: 15166020."
2004
100
iCTNet - integrated Complex Traits Network
http://flux.cs.queensu.ca/ictnet
"An open-source Cytoscape plugin that integrates several data sources to allow automated and systematic creation of networks with up to five layers of omics information: phenotype-SNP association, PPIs, disease-tissue, tissue-gene, and drug-gene relationships. It allows the generation of general or specific network views with diverse options for many diseases. Built-in tools are provided to prioritize candidate genes and create modules of specific phenotypes."
"Wang L, Khankhanian P, Baranzini SE, Mousavi P. iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks. BMC Bioinformatics. 2011 Sep 26;12:380. PubMed PMID: 21943367; PubMed Central PMCID: PMC3190406."
2011
100
iHOP - Information Hyperlinked over Proteins
http://www.ihop-net.org
"An information extraction system for protein information including PPIs, from PubMed. Build interactomes (e.g., interactomes related to a tissue/disease) using sentences related to PPIs. User interaface parameters allowed. Interactions can be restricted to a given experimental evidence."
"Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet. 2004 Jul;36(7):664. PubMed PMID: 15226743."
2004
100
IM Browser - Interaction Map Browser
http://proteome.wayne.edu/PIMdb.html
A web-based application designed to explore and visualize interaction data stored in a database. The tool connects to either Drosophila Interactions Database or Campylobacter jejuni Interactions Database as specified by the user.
"Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics. 2006 Apr 7;7:195. PubMed PMID: 16603075; PubMed Central PMCID: PMC1458360."
2006
100
InnateDB - A Knowledge Resource For Innate Immunity Interactions & Pathways
http://www.innatedb.ca
"A publicly available, manually curated database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection. The database also integrates known interactions and pathways from major public databases together with manually-curated data. It has integrated various bioinformatics resources, for network visualization, pathway analysis, orthologous interaction network construction and tools to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists to explore their data in a more systems-oriented manner."
"Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol. 2008;4:218. Epub 2008 Sep 2. PubMed PMID: 18766178; PubMed Central PMCID: PMC2564732."
2008
100
IntAct
http://www.ebi.ac.uk/intact
"A database that provides protein-protein interactions of experimental importance. Protein-protein interactions for few specific diseases are available. Protein interactions specific to a biological process (e.g., apoptosis, cell cycle) can also be obtained. Provides interactions along with their functional associations. Interactions can be restricted to a given experimental evidence. Provides interactions related to cancer. Provides protein-drug interactions. User interaface parameters can be implied to the input."
"Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R. IntAct: an open source molecular interaction database. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5. PubMed PMID: 14681455; PubMed Central PMCID: PMC308786."
2004
100
INTEGRATOR
http://bioverse.compbio.washington.edu/integrator
"A collection of interactive, graphical search tools for exploring PPI networks across many genomes. It provides both single and multiple protein search options. The interface provides animated local network views, rapid subgraph manipulation, and cross-referencing of functional annotations."
"Chang AN, McDermott J, Frazier Z, Guerquin M, Samudrala R. INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics. 2006 Mar 16;7:146. PubMed PMID: 16542421; PubMed Central PMCID: PMC1459205."
2006
100
Interactorium
http://www.interactorium.net
"A platform built to display very complex networks of up to 40,000 proteins or 6000 multi-protein complexes in a virtual 3D cell and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. "
"Widjaja YY, Pang CN, Li SS, Wilkins MR, Lambert TD. The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell. Proteomics. 2009 Dec;9(23):5309-15. PubMed PMID: 19798670."
2009
100
InterMitoBase
http://mcube.nju.edu.cn/cgi-bin/intermitobase/home.pl
"An annotated database and analysis platform of PPIs for human mitochondria. It collects PPIs by literature mining from PubMed and from various other resources including KEGG, BioGRID, HPRD, DIP and IntAct. It features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified."
"Gu Z, Li J, Gao S, Gong M, Wang J, Xu H, Zhang C, Wang J. InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. BMC Genomics. 2011 Jun 30;12:335. PubMed PMID: 21718467; PubMed Central PMCID: PMC3142533."
2011
100
Interolog/Regulog Database
http://interolog.gersteinlab.org
A database to find possible physical or regulatory interaction partners by interolog mapping. It finds the regulogs based on conserved regulatory relationship between proteins across different species.
"Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004 Jun;14(6):1107-18. PubMed PMID: 15173116; PubMed Central PMCID: PMC419789."
2004
100
InterPreTS - Interaction Prediction through Tertiary Structure
http://www.russell.embl.de/interprets
"A web-based tool for predicting protein interaction through tertiary structure of proteins. Given a set of protein sequences (in fasta format), this tool will use BLAST to find homologues of known structure for all pairs and then evaluate the suitability of those templates for modelling the interaction using the method described in Aloy & Russell, 2002 and Aloy & Russell, 2003."
"Aloy P, Russell RB. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics. 2003 Jan;19(1):161-2. PubMed PMID: 12499311."
2003
100
InterViewer
http://interviewer.inha.ac.kr
"An algorithm for visualizing large-scale protein interaction networks. Advantages of InterViewer over classical graph drawing methods include: It is faster, it can directly visualize data from protein interaction databases, and it provides several operations for effectively exploring large-scale protein interaction networks."
"Ju BH, Park B, Park JH, Han K. Visualization and analysis of protein interactions. Bioinformatics. 2003 Jan 22;19(2):317-8. PubMed PMID: 12538268."
2003
100
IntNetDB - Integrated Network Database
http://hanlab.genetics.ac.cn/IntNetDB.htm
"A database of human PPIs, computationally predicted through Bayesian analysis by integrating large-scale physical PPIs, protein domain assignments, gene co-expression data, genetic interactions, gene context information and biological function annotations from human and other model organisms."
"Xia K, Dong D, Han JD. IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics. 2006 Nov 18;7:508. PubMed PMID: 17112386; PubMed Central PMCID: PMC1661597."
2006
100
iRefIndex
http://irefindex.uio.no
"A database that provides non-redundant index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. iRefWeb provides a searchable web interface to the iRefIndex."
"Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics. 2008 Sep 30;9:405. PubMed PMID: 18823568; PubMed Central PMCID: PMC2573892."
2008
100
iRefR
http://cran.r-project.org/web/packages/iRefR
"An R package to manipulate the iRefIndex protein interaction database. It includes tools for selecting specific subsets of interest from the iRefIndex, by organism, source database, experimental method, etc. "
"Mora A, Donaldson IM. iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. BMC Bioinformatics. 2011 Nov 24;12(1):455. [Epub ahead of print] PubMed PMID: 22115179."
2011
100
iRefWeb
http://wodaklab.org/iRefWeb
"A web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. It enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Furthermore, it compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies."
"Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford). 2010 Oct 12;2010:baq023. Print 2010. PubMed PMID: 20940177; PubMed Central PMCID: PMC2963317."
2010
100
JNets
http://www.manchester.ac.uk/bioinformatics/jnets
A network visualization and analysis tool that can be used for visualizing and analyzing protein interaction networks as well as other type of networks. It is available as a standalone application or an applet.
"Macpherson JI, Pinney JW, Robertson DL. JNets: exploring networks by integrating annotation. BMC Bioinformatics. 2009 Mar 26;10:95. PubMed PMID: 19323810; PubMed Central PMCID: PMC2674432."
2009
100
KDBI - Kinetic Data of Biomolecular Interaction
http://bidd.nus.edu.sg/group/kdbi/kdbi.asp
"A collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature."
"Ji ZL, Chen X, Zhen CJ, Yao LX, Han LY, Yeo WK, Chung PC, Puy HS, Tay YT, Muhammad A, Chen YZ. KDBI: Kinetic Data of Bio molecular Interactions database. Nucleic Acids Res. 2003 Jan 1;31(1):255-7. PubMed PMID: 12519995; PubMed Central PMCID: PMC165514."
2003
100
KUPS - The University of Kansas Proteomics Service
http://www.ittc.ku.edu/chenlab/kups
"A source of high-quality PPI data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. It combines three manually curated PPI databases (i.e, IntAct, MINT and HPRD ) with features and annotations retrieved from UniProt , Position Specific Scoring Matrix (PSSM) with non-redundent database from NCBI PSI-BLAST , and amino acid scaling features from the Amino Acid Index database ."
"Chen XW, Jeong JC, Dermyer P. KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. Nucleic Acids Res. 2011 Jan;39(Database issue):D750-4. Epub 2010 Oct 15. PubMed PMID: 20952400; PubMed Central PMCID: PMC3013794."
2010
100
Lists2Networks
http://www.lists2networks.org
"A web-based system that allows users to perform integrated analysis of the lists of mammalian genes/proteins. The system includes web-based tools to expand lists using existing mammalian networks of PPIs, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, Gene Ontology terms, kinase-substrate, microRNA-mRAN, and PPIs, metabolites, and protein domains."
"Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics. 2010 Feb 12;11:87. PubMed PMID: 20152038; PubMed Central PMCID: PMC2843617."
2010
100
LR_PPI
http://www.csbio.sjtu.edu.cn/bioinf/LR_PPI
A resource specific to human PPIs. Provides interactions based on the proteins' sequence conservation/similarity.
"Pan XY, Zhang YN, Shen HB. Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features. J Proteome Res. 2010 Oct 1;9(10):4992-5001. PubMed PMID: 20698572."
2010
100
MAPPIS - Multiple Alignment of Protein-Protein InterfaceS
http://bioinfo3d.cs.tau.ac.il/MAPPIS
"A method for multiple structural alignment of PPIs. It performs multiple alignment of protein-protein interfaces, which are regions of interaction between two protein molecules. It recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein-protein associations."
"Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol. 2007 Oct 9;5:43. PubMed PMID: 17925020; PubMed Central PMCID: PMC2231411."
2007
100
MATISSE - Module Analysis via Topology of Interactions and Similarity Sets
http://acgt.cs.tau.ac.il/matisse
"A program for detection of functional modules using interaction networks and expression data. Currently it supports the analysis of data from the species H. sapiens, M. musculus, S. cerevisiae, D. melanogaster, and C. elegans."
"Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol. 2007 Jan 26;1:8. PubMed PMID: 17408515; PubMed Central PMCID: PMC1839897."
2007
100
MatrixDB - Extracellular Matrix interactions DataBase
http://matrixdb.ibcp.fr
"A resource that provides protein interaction data by curation and text-mining and also from other databases, specifically for extracellular matrix proteins. Provides options to build interactomes."
"Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S. MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics. 2009 Mar 1;25(5):690-1. Epub 2009 Jan 15. PubMed PMID: 19147664; PubMed Central PMCID: PMC2647840."
2009
100
Medusa
http://www.bork.embl.de/medusa
A Java application for visualization and manipulation of protein interaction graphs.
"Hooper SD, Bork P. Medusa: a simple tool for interaction graph analysis. Bioinformatics. 2005 Dec 15;21(24):4432-3. Epub 2005 Sep 27. PubMed PMID: 16188923."
2005
100
MeInfoText - associated gene methylation and cancer information from text mining
http://mit.lifescience.ntu.edu.tw
"A database that presents comprehensive association information about gene methylation and cancer, based on text-mining of literature. It also has integrated protein-interaction and biological pathway information collected from the other resources. "
"Fang YC, Huang HC, Juan HF. MeInfoText: associated gene methylation and cancer information from text mining. BMC Bioinformatics. 2008 Jan 14;9:22. PubMed PMID: 18194557; PubMed Central PMCID: PMC2258285."
2008
100
Meta-PPISP - meta web server for protein-protein interaction site prediction
http://pipe.scs.fsu.edu/meta-ppisp
"A resource that can predict PPI sites based on three individual web servers: cons-PPISP, Promate and PINUP."
"Qin S, Zhou HX. meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics. 2007 Dec 15;23(24):3386-7. Epub 2007 Sep 25. PubMed PMID: 17895276."
2007
100
MIM PathVisio
http://discover.nci.nih.gov/mim/mim_pathvisio.html
"A plugin for creating and editing Molecular Interaction Maps (MIMs). It helps the users draw diagrams of bioregulatory networks according to the MIM notation, construction of complex MIM diagrams with the ability to annotate diagram elements with comments, literature references and links to external databases."
"Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW. PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics. 2011 Aug 1;27(15):2165-6. Epub 2011 Jun 2. PubMed PMID: 21636591; PubMed Central PMCID: PMC3137219."
2011
100
MiMI - Michigan Molecular Interaction
http://mimi.ncibi.org
Collects protein interaction data from multiple PPI databases. Provides interactions along with their functional associations.
"Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720."
2006
100
MINT - Molecular INTeraction
http://mint.bio.uniroma2.it
A database that provides PPIs of experimental importance. It also identifies interactions among the given list of proteins. Provides options to curate data for the database.
"Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett. 2002 Feb 20;513(1):135-40. Review. PubMed PMID: 11911893."
2002
100
miPALM - Module Inference by Parametric Local Modularity
http://www.healthcare.uiowa.edu/labs/tan/miPALM.htm
"An algorithm for detecting protein complexes from large PPI networks. The algorithm uses a novel graph theoretic measure, parametric local modularity, to identify highly connected sub-networks as candidate protein complexes. "
"Kim J, Tan K. Discover protein complexes in protein-protein interaction networks using parametric local modularity. BMC Bioinformatics. 2010 Oct 19;11:521. PubMed PMID: 20958996; PubMed Central PMCID: PMC2974752."
2010
100
MiPPI - Microbial Protein-Protein Interactions
http://mippi.ornl.gov
A resource specific to microbial (R. palustris & S. oneidensis) protein interactions derived from experimental data.
Not available
Not available
100
MIPS-MPPI - MIPS Mammalian Protein-Protein Interaction
http://mips.helmholtz-muenchen.de/proj/ppi
A web-resource specific to mammalian PPIs. Provides interactions for a specific disease/biological process. Provides interactions along with their functional associations. Interactions can be restricted to a specific experimental evidence.
"Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics. 2005 Mar;21(6):832-4. Epub 2004 Nov 5. PubMed PMID: 15531608"
2004
100
MitoInteractome - Mitochondrial Protein Interactome Database
http://mitointeractome.kobic.kr
"A resource specific to mitochondrial PPIs. Predicts interactions based on the domain/interfaces/sites. Provides inferred interactions (e.g., human interactions inferred from mouse & rat)."
"Reja R, Venkatakrishnan AJ, Lee J, Kim BC, Ryu JW, Gong S, Bhak J, Park D. MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. BMC Genomics. 2009 Dec 3;10 Suppl 3:S20. PubMed PMID: 19958484; PubMed Central PMCID: PMC2788373."
2009
100
MitoP2
http://ihg.gsf.de/mitop2
A resource specific to yeast mitochondrial PPIs. Collects interaction data from multiple databases.
"Andreoli C, Prokisch H, Hörtnagel K, Mueller JC, Munsterkotter M, Scharfe C, Meitinger T. MitoP2, an integrated database on mitochondrial proteins in yeast and man. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D459-62. PubMed PMID: 14681457; PubMed Central PMCID: PMC308871."
2004
100
MitoProteome
http://www.mitoproteome.org/database
"A database of human mitochondrial protein sequences, where information obtained from a comprehensive curation of public databases as well as from direct experimental evidence. It contains both mitochondrial- and nuclear-encoded protein sequences. Each protein is annotated with data extracted from external databases, including protein interaction data extracted from MINT and DIP databases."
"Cotter D, Guda P, Fahy E, Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D463-7. PubMed PMID: 14681458; PubMed Central PMCID: PMC308782."
2004
100
MODEVO - Modularity and evolution of protein networks
http://bioputer.mimuw.edu.pl/modevo
"Cytoscape plugins, that can be used to map evolving protein interaction networks at the module level. Affinity propagation (AP) algorithm for graph clustering to decompose networks into coherent modules, implemented by APCluster plugin. Visualize selected modules in consecutive evolutionary stages, implemented by NetworkEvolution plugin."
"Wozniak M, Tiuryn J, Dutkowski J. MODEVO: exploring modularity and evolution of protein interaction networks. Bioinformatics. 2010 Jul 15;26(14):1790-1. Epub 2010 May 27. PubMed PMID: 20507893."
2010
100
"A platform for prediction of fold using protein interactions. Uses both sequence similarity and PPIs to assign a Structural Classification Of Proteins (SCOP) fold and a family classification to uncharacterized proteins. The new version of ModLink, called ModLink includes an improved procedure for extrapolating links that iteratively varies the number of interactions required to consider a protein as a hub."
"Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink: improving fold recognition by using protein-protein interactions. Bioinformatics. 2009 Jun 15;25(12):1506-12. Epub 2009 Apr 8. PubMed PMID: 19357100; PubMed Central PMCID: PMC2687990."
2009
100
ModuleSearch - Finding modules in protein-protein interaction networks
http://bclab.inha.ac.kr/ModuleSearch
"A resource that can be used to identify and visualize functional modules in a given PPI network. In a given interaction network, it also finds the overlapping modules. It helps in identifying densely connected subgraph that provides useful information to predict the function or protein complex of uncharacterized proteins. Also finds cliques and near-cliques in a PPI network."
"Cui G, Shrestha R, Han K. ModuleSearch: finding functional modules in a protein-protein interaction network. Comput Methods Biomech Biomed Engin. 2011 Aug 9. [Epub ahead of print] PubMed PMID: 21827286."
2011
100
Moksiskaan
http://csbi.ltdk.helsinki.fi/moksiskaan
"A platform (Moksiskaan) that integrates pathway, PPI, genome and literature mining data to result in comprehensive networks for a list of genes or proteins. It can also generate hypothetical pathways for genes or proteins as well as estimate their activation statuses using regulation information in pathway repositories. It can be used to combine various existing databases and find out the biological relationships between the genes of interest and to predict their interactions. "
"Laakso M, Hautaniemi S. Integrative platform to translate gene sets to networks. Bioinformatics. 2010 Jul 15;26(14):1802-3. Epub 2010 May 27. PubMed PMID: 20507894."
2010
100
Molecule Pages - A comprehensive signaling database
http://www.signaling-gateway.org/molecule
"A database that provides essential information on proteins involved in cellular signaling. The protein information i.e., ""Molecule pages"" contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. Also supplemented with data of PPIs, post-translational modifications, subcellular localization and biological function."
"Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S. The Molecule Pages database. Nature. 2002 Dec 12;420(6916):716-7. PubMed PMID: 12478304."
2002
100
MoReNet - Mouse Retina Network
http://bioinfo.wilmer.jhu.edu/morenet
"A tissue (retina) specific functional gene network, which integrates different types of available biological data supporting functional relationships of genes. Constructs the network of genes by Bayesian Network method, by employing Gene Ontology, KEGG pathway annotation, PPI and microarray data."
"Hu J, Wan J, Hackler L Jr, Zack DJ, Qian J. Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. Bioinformatics. 2010 Sep 15;26(18):2289-97. Epub 2010 Jul 8. PubMed PMID: 20616386; PubMed Central PMCID: PMC2935398."
2010
100
mouseNET
http://mouseNET.princeton.edu
"A functional network for the laboratory mouse developed based on Bayesian integration of diverse genetic and functional genomic data. Also retrieves disease related genes, for a given gene along with the interactions. Helps in predicting novel functional assignments and network components. Provides the significant Gene Ontology terms, associated with the network. Shows the network in a graphical representation of the network. Provides the evidences for the interactions shown in the network."
"Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 2008 Sep 26;4(9):e1000165. PubMed PMID: 18818725; PubMed Central PMCID: PMC2527685."
2008
100
MoVIN
http://www.biocomputing.it/MOVIN
"A sever that can be used to analyse user-supplied datasets. It analyses and assigns a confidence score to Yeast PPI maps. It contains pre-processed data for four yeast PPI datasets and the results of their statistical analysis. Provides the common motifs, Pfam domains and Gene Ontology annotations in groups of proteins with a common binding partner. Helps to investigate the properties of the interacting proteins. "
"Marcatili P, Bussotti G, Tramontano A. The MoVIN server for the analysis of protein interaction networks. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S11. PubMed PMID: 18387199; PubMed Central PMCID: PMC2323660."
2008
100
MPact - Representation of Interaction Data at MIPS
http://mips.gsf.de/genre/proj/mpact
"A manually curated database on yeast PPIs at MIPS (Munich Information Center for Protein Sequences). It is a repository of biological interactions, and support the PSI-MI standard, for both downloading and uploading data. Provides the interaction network in graphical representation also."
"Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stümpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D436-41. PubMed PMID: 16381906; PubMed Central PMCID: PMC1347366."
2006
100
MPID - Magnaporthe grisea Protein-protein Interaction Database
http://bioinformatics.cau.edu.cn/zzd_lab/MPID.html
"A database of predicted PPI network in rice blast fungus. Inferring PPIs in M.grisea from model organisms protein interaction datasets, based on orthologous proteins in M.grisea. The orthologous proteins were identified through InParanoid algorithm. The Gene Ontology annotations for M.grisea were generated through InterproSCAN."
"He F, Zhang Y, Chen H, Zhang Z, Peng YL. The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics. 2008 Nov 2;9:519. PubMed PMID: 18976500; PubMed Central PMCID: PMC2601049."
2008
100
MPIDB - Microbial Protein Interaction DataBase
http://www.jcvi.org/mpidb
A database specific to bacterial PPIs. Gets similar protein interactions among species.
"Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, Uetz P. MPIDB: the microbial protein interaction database. Bioinformatics. 2008 Aug 1;24(15):1743-4. Epub 2008 Jun 13. PubMed PMID: 18556668; PubMed Central PMCID: PMC2638870."
2008
100
MPID-T - MHC-Peptide Interaction Database-TR
http://biolinfo.org/mpid-t2
A database specific to MHC-peptide interactions. Provides interactions based on the protein structure. Provides the kinetics/thermodynamics of the interactions. 3D view of the PPI data available.
"Govindarajan KR, Kangueane P, Tan TW, Ranganathan S. MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics. 2003 Jan 22;19(2):309-10. PubMed PMID: 12538264."
2003
100
MppDB - Mouse protein-protein interaction DataBase
http://bio.scu.edu.cn/mppi
"A database specific to mouse PPIs. Collects interaction data from multiple databases. Predicts interaction based on co-expression, genomic data, Gene Ontology, domain/interfaces/sites and gene co-evolution. "
"Li X, Cai H, Xu J, Ying S, Zhang Y. A mouse protein interactome through combined literature mining with multiple sources of interaction evidence. Amino Acids. 2010 Apr;38(4):1237-52. Epub 2009 Aug 8. PubMed PMID: 19669079."
2009
100
MPSQ - Multi-Protein-States Query
http://mpsq.biosino.org
"A web-based tool for the discovery of protein states (e.g. biological interactions, covalent modifications, cellular localizations) and search for enriched state transition network maps (NMs). A graphical visualization of the returned NM helps for easy understanding and to guide further analysis."
"Zheng S, Sheng J, Wang C, Wang X, Yu Y, Li Y, Michie A, Dai J, Zhong Y, Hao P, Liu L, Li Y. MPSQ: a web tool for protein-state searching. Bioinformatics. 2008 Oct 15;24(20):2412-3. Epub 2008 Aug 12. PubMed PMID: 18697766."
2008
100
MPTV - Membrane Protein Topology Viewer
http://www.bioforscher.de/mptv.htm
"A software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. Gives clues for the interpretation of protein structure and its underlying molecular interactions. Integrated various bioinformatic features which further assists in determining the membrane protein folding, structure, stability and function. "
"Mueller F, Muller DJ, Labudde D. Analysis assistant for single-molecule force spectroscopy data on membrane proteins--MPTV. Bioinformatics. 2006 Jul 15;22(14):1796-9. Epub 2006 Apr 10. PubMed PMID: 16606684."
2006
100
Narada - Annotation Patterns in Biological Networks
http://www.cs.purdue.edu/homes/jpandey/narada
"A PPI analysis tool, deriving overrepresented annotation patterns in biological networks, from annotation of individual molecules. Identifies the functional annotation of pathways for a given molecular interaction network. Also helps in identifying novel pathways."
"Pandey J, Koyutürk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. Bioinformatics. 2007 Jul 1;23(13):i377-86. PubMed PMID: 17646320."
2007
100
Nascent - Protein-Protein Physical Interaction Network Originating Tool
http://nascent.pitgroup.org
"A protein-protein physical interaction network originating tool. Network construction is predicted based on gene names and sequence similarity. It searches for proteins of source organism which are in physical interaction by the IntAct database. Majority of the data corresponds to Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli and Mus musculus."
"Banky D, Ordog R, Grolmusz V. NASCENT: an automatic protein interaction network generation tool for non-model organisms. Bioinformation. 2009 Apr 24;3(8):361-3. PubMed PMID: 19707301; PubMed Central PMCID: PMC2720673."
2009
100
A tool for for the 2D and 3D visualization of PPI or biological networks. It includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. It supports community-developed data formats such as PSI-XML, BioPax and GML, is platform-independent and is extensible through a plug-in architecture.
Not available
2009
100
NCPI - Neurospora crassa Protein Interactome database
http://protein.cau.edu.cn/ncpi
A database of predicted PPIs in Neurospora crassa species. Predictions are based on the interolog method and the domain interaction-based method.
"Wang TY, He F, Hu QW, Zhang Z. A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa. Mol Biosyst. 2011 Jul;7(7):2278-85. Epub 2011 May 16. PubMed PMID: 21584303."
2011
100
NetAge
http://netage-project.org
"NetAge is an online database and also has network analysis tools for biogerontological research. It gives microRNA-regulated PPI networks which are involved in complex processes of aging and age-related diseases (ARDs), and ultimately in the determination of longevity. Currently includes five species including human and mouse. The interactions include all the physical and genetic interactions reported in the BioGRID database, as well as all the miRNA-gene interactions from the TarBase database. The database also provides overlapping networks, cellular localization and function for the queried gene/protein."
"Tacutu R, Budovsky A, Fraifeld VE. The NetAge database: a compendium of networks for longevity, age-related diseases and associated processes. Biogerontology. 2010 Aug;11(4):513-22. Epub 2010 Feb 26. PubMed PMID: 20186480."
2010
100
NetAlign - Network Alignment
http://netalign.ustc.edu.cn/NetAlign
A web-server for comparative analysis of protein interaction networks. Compares a user-specified query protein interaction network with a target protein interaction network to identify conserved network substructures.
"Liang Z, Xu M, Teng M, Niu L. NetAlign: a web-based tool for comparison of protein interaction networks. Bioinformatics. 2006 Sep 1;22(17):2175-7. Epub 2006 Jun 9. PubMed PMID: 16766562."
2006
100
NetAtlas
http://sourceforge.net/projects/netatlas
A tool that uses tissue gene expression data to identify cellular signaling network.
"Yang L, Walker JR, Hogenesch JB, Thomas RS. NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression. In Silico Biol. 2008;8(1):47-52. PubMed PMID: 18430989."
2008
100
Netmotsa
http://code.google.com/p/netmotsa
"A computational method for identifying the ligand peptides of ""peptide recognition modules"" by combining protein sequence information and observed physical interactions into a simple probabilistic model and from it derive an interaction-mediated de novo motif-finding framework. It identifies motifs with sensitivity and specificity which helps in predicting protein-peptide interactions."
"Reiss DJ, Schwikowski B. Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics. 2004 Aug 4;20 Suppl 1:i274-82. PubMed PMID: 15262809."
2004
100
NetPath
http://www.netpath.org
A resource of curated human signaling pathways. It also includes PPIs collected from literature.
"Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010 Jan 12;11(1):R3. PubMed PMID: 20067622; PubMed Central PMCID: PMC2847715."
2010
100
NetPro - Knowledgebase of Molecular Interactions
http://www.interactions.net.in
"Manually curated database of molecular interactions. It also covers several other type of molecular interactions other than protein-protein, such as protein-RNA, protein-DNA etc."
Not available
Not available
100
Netview
http://netview.tigem.it
"A web-based tool that allow end users to explore the human and mouse gene regulatory networks. The networks are developed based on a mutual information (MI) reverse-engineering approach to quantify the extent to which the mRNA levels of two genes are related to each other across the dataset. The tool provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork, for the queried gene/protein. Gives a list of predicted interactions that are found to be statistically significant. It also has ""Gene Ontology prediction"" tool and ""gene signature analysis"" tool. Also allows the user to select a tissue, and visualize those interactions that connect genes significantly expressed into the selected tissue. Currently includes data for human and mouse species. For a given list of genes, it provides a list of transcription factors that significantly regulates a sub-set of given genes."
"Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D. Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res. 2011 Nov 1;39(20):8677-88. Epub 2011 Jul 23. PubMed PMID: 21785136; PubMed Central PMCID: PMC3203605."
2011
100
Network legos
http://bioinformatics.cs.vt.edu/ murali/software/network-lego
"A computational approach to identify building blocks of molecular interaction networks by: (i) integrating gene expression measurements for a particular disease state (e.g., leukemia) or experimental condition (e.g., treatment with growth serum) with molecular interactions to reveal an active network, which is the network of interactions active in the cell in that disease state or condition; and (ii) systematically combining active networks computed for different experimental conditions using set-theoretic formulae to reveal network legos, which are modules of coherently interacting genes and gene products in the wiring diagram. "
"Murali TM, Rivera CG. Network legos: building blocks of cellular wiring diagrams. Lecture Notes in Computer Science, 2007, Volume 4453/2007, 47-61."
2007
100
NetworkAnalyzer
http://med.bioinf.mpi-inf.mpg.de/networkanalyzer
"A Cytoscape plugin for the analysis and visualization of molecular interaction networks. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths."
"Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics. 2008 Jan 15;24(2):282-4. Epub 2007 Nov 15. PubMed PMID: 18006545."
2007
100
NetworkBLAST
http://www.cs.tau.ac.il/~bnet/networkblast.htm
A web-server that provides a platform for identifying protein complexes in PPI networks. Can be used to analyze a single network or two networks from different species and gives a set of putative complexes that are evolutionarily conserved across the two networks. User can also BLAST data for two species proteins.
"Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 2008 Feb 15;24(4):594-6. Epub 2008 Jan 2. PubMed PMID: 18174180."
2008
100
NetworKIN
http://networkin.info
"A database for exploring cellular phosphorylation networks. It integrates consensus substrate motifs with context modelling for improved prediction of cellular kinase-substrate relations. It can be used to query precomputed kinase-substrate relations or obtain predictions on novel phosphoproteins. User can browse or search, and investigate predictions made using the NetworKIN algorithm. Currenlty focussed on human kinases."
"Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14. PubMed PMID: 17570479; PubMed Central PMCID: PMC2692296."
2007
100
NIA Mouse Protein-Protein Interaction Database
http://lgsun.grc.nia.nih.gov/mppi
"A database of Hosts inferred PPIs in Mus musculus by using two approaches, i) identifying mouse orthologs of interacting proteins (interologs) based on the experimental PPI data from other organisms and ii) analyzing frequency of mouse ortholog co-occurrence in predicted operons of bacteria. Also filteres out the possible false-positives in the predicted interactions using the phylogenetic profiles. Filtering method also considers the frequency of interacting protein-pairs coexpressed in the same cells/tissues in GEO database as well as the frequency of interacting protein-pairs shared the similar Gene Ontology terms for biological processes and cellular localizations."
"Yellaboina S, Dudekula DB, Ko MSh. Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics. 2008 Oct 8;9:465. PubMed PMID: 18842131; PubMed Central PMCID: PMC2571111."
2008
100
NOXCLASS
http://noxclass.bioinf.mpi-inf.mpg.de
"A web-server for distinguishing protein interactions to obligate, non-obligate and crystal packing interactions. NOXclass resulted from combining six interface properties using a support vector machine algorithm. A dataset of 243 protein interactions were used to investigate the six poperties. The six properties include interface area, interface area ratio, area-based amino acid composition of protein-protein interface, correlation between area-based amino acid compositions of interface and the rest of protein surface, gap volume index and conservation score of protein-protein interface."
"Zhu H, Domingues FS, Sommer I, Lengauer T. NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics. 2006 Jan 19;7:27. PubMed PMID: 16423290; PubMed Central PMCID: PMC1386716"
2006
100
NURSA - Nuclear Receptor Signaling Atlas
http://www.nursa.org
"A consortium developed with the aim to utilize classical approaches to validate existing hypotheses and exploit new and emerging technologies to formulate and test new hypotheses that might elucidate the program of nuclear receptor (NR) structure, function, and role in disease. The main goals for the NURSA consortium are to: 1) establish the mechanistic principles of NR function, 2) characterize NR-coregulator complex formation and regulation, 3) map protein-protein interactions for coregulators, 4) identify candidate downstream target genes of NR action, 5) identify target tissue expression of NRs, 6) understand the regulation of NR expression and, 7) integrate existing and emerging information through NURSA bioinformatics tools. It gives an overview of expression, diseases, phenotypes, orthologs, interactions, ligands, transciptomics, cistromics and literature for the selected or queried NR."
"Margolis RN, Evans RM, O'Malley BW; NURSA Atlas Consortium. The Nuclear Receptor Signaling Atlas: development of a functional atlas of nuclear receptors. Mol Endocrinol. 2005 Oct;19(10):2433-6. Epub 2005 Jul 28. PubMed PMID: 16051673."
2005
100
OpenDMAP - Open source Direct Memory Access Parser
http://opendmap.sourceforge.net
"An information extraction system which is ontology-driven, and with rule-based concept analysis. It processes texts to recognize concepts and relationships from a knowledge-base. OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport), PPI assertions (interaction) and assertions that a gene is expressed in a cell type (expression). It advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles."
"Hunter L, Lu Z, Firby J, Baumgartner WA Jr, Johnson HL, Ogren PV, Cohen KB. OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics. 2008 Jan 31;9:78. PubMed PMID: 18237434; PubMed Central PMCID: PMC2275248."
2008
100
OpenPPI_predictor
http://tools.neb.com/~posfai/OpenPPI_predictor.zip
"A tool for prediction of genome wide PPI network based on ortholog information. It generates putative protein-protein interaction network for target genomes. The tool uses the orthologous interactome network data from a related, experimentally studied organism."
"Pedamallu CS, Posfai J. Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information. Source Code Biol Med. 2010 Aug 4;5:8. PubMed PMID: 20684769; PubMed Central PMCID: PMC2924336."
2010
100
OrthoNets
http://wodaklab.org/orthonets
"A Cytoscape plugin that displays PPI networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. It enables the simultaneous visualization of PPI networks in multiple organisms, using information aggregated in Disease Annotated Chromatin Epigenetics Resource (DAnCER) and iRefWeb/iRefIndex. Also allows PPI networks derived from experiments to be overlaid on those extracted from public databases, supporting the identification and verification of new interactors. "
"Hao Y, Merkoulovitch A, Vlasblom J, Pu S, Turinsky AL, Roudeva D, Turner B, Greenblatt J, Wodak SJ. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics. 2011 Mar 15;27(6):883-4. Epub 2011 Jan 20. PubMed PMID: 21257609; PubMed Central PMCID: PMC3051336."
2011
100
Osprey
http://biodata.mshri.on.ca/osprey
A software platform for visualization and manipulation of complex interaction networks. It builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.
"Breitkreutz BJ, Stark C, Tyers M. Osprey: a network visualization system. Genome Biol. 2003;4(3):R22. Epub 2003 Feb 27. PubMed PMID: 12620107; PubMed Central PMCID: PMC153462."
2003
100
P.R.I.S.M. - PRotein Interactions by Structural Matching
http://prism.ccbb.ku.edu.tr/prism
A web-server to explore protein interfaces and predict PPIs. It predicts PPIs by combining structure and sequence conservation in protein interfaces. It has several options for querying and browsing the server.
"Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics. 2005 Jun 15;21(12):2850-5. Epub 2005 Apr 26. PubMed PMID: 15855251."
2005
100
p53 knowledgebase
http://p53.bii.a-star.edu.sg
"A web portal dedicated to p53, incorporating visualization and analysis tools that integrates information from the published literature with other manually curated information. This includes curated information on sequence, structure, mutation, polymorphisms, PPIs, transcription factors, transcriptional targets, pathways, antibodies and post-translational modifications that involve p53. "
"Lim YP, Lim TT, Chan YL, Song AC, Yeo BH, Vojtesek B, Coomber D, Rajagopal G, Lane D. The p53 knowledgebase: an integrated information resource for p53 research. Oncogene. 2007 Mar 8;26(11):1517-21. Epub 2006 Sep 4. PubMed PMID: 16953220."
2007
100
PAComplex
http://PAcomplex.life.nctu.edu.tw
"A peptide antigen search server, useful for analyzing novel peptide antigens and inferring homologous peptides. It investigates both peptide-major histocompatibility complexes (pMHC) and peptide - T-cell receptors (TCR) interfaces to infer peptide antigens and homologous peptide antigens of a query. PAComplex shows the detailed atomic interactions, binding models, homologous peptide antigen, joint Z-value of each peptide candidate, for a given query. Also gives Knowledge-based scoring matrix for peptide-MHC interactions and peptide-TCR interactions."
"Liu IH, Lo YS, Yang JM. PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W254-60. Epub 2011 Jun 11. PubMed PMID: 21666259; PubMed Central PMCID: PMC3125798."
2011
100
PAIR - Predicted Arabidopsis Interactome Resource
http://www.cls.zju.edu.cn/pair
"A resource that contains experimentally reported molecular interactions in Arabidopsis thaliana together with predicted interactions with high reliability. It predicts interactions by support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). Provides rich annotation on the relationships between two proteins and also integrated graphical interaction network browser that helps in mining of specific pathways. Database allows many options to query such as BLAST, pair of proteins, interologs, other than common query by protein."
"Lin M, Hu B, Chen L, Sun P, Fan Y, Wu P, Chen X. Computational identification of potential molecular interactions in Arabidopsis. Plant Physiol. 2009 Sep;151(1):34-46. Epub 2009 Jul 10. PubMed PMID: 19592425; PubMed Central PMCID: PMC2735983."
2009
100
PARPs-DB - poly(ADP-ribose) polymerases - Database
http://parpdb.sourceforge.net
"A web-based tool for data analysis and management of mass spectrometry data. Features of the tool include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. The software has links to public databases including PPIs databases such as BIND, DIP and HPRD. It also has a protein-protein interaction viewer to visualize interaction networks."
"Droit A, Hunter JM, Rouleau M, Ethier C, Picard-Cloutier A, Bourgais D, Poirier GG. PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. BMC Bioinformatics. 2007 Dec 19;8:483. PubMed PMID: 18093328; PubMed Central PMCID: PMC2266781."
2007
100
PatchDock - Molecular Docking Algorithm Based on Shape Complementarity Principles
http://bioinfo3d.cs.tau.ac.il/PatchDock
"A molecular docking algorithm that performs structure prediction of protein-protein and protein-small molecule complexes. The inputs are either protein PDB codes or uploaded protein structures or two molecules of any type: proteins, DNA, peptides, drugs. It gives a list of potential complexes sorted by shape complementarity criteria for the submitted query. Two tools: FireDock - fast interaction refinement in molecular docking and SymmDock - an algorithm for prediction of complexes with Cn symmetry are integrated in the PatchDock."
"Duhovny D, Nussinov R, Wolfson HJ. Efficient Unbound Docking of Rigid Molecules. In Gusfield et al., Ed. Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics(WABI) Rome, Italy, Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag, 2002."
2002
100
PathArt
http://www.jubilantbiosys.com/pathart.html
A database of signal transduction and metabolic pathways across many diseases and physiologies including protein-protein interactions maps. It has three modules: Core PathArt - for pathways; Interaction Maps - for interactions; Druggable Targets Database - for finding out drug and inhibitor information. The PPIs are collected by manually curating full text article in case of PathArt and abstracts in Interaction maps.
Not available
Not available
100
PathBinder
http://www.metnetdb.org/pathbinder
"A tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules from MEDLINE database, based on an algorithm to extract biomolecular interactions from texts. The algorithm was developed by manually analyzing syntactic and semantic properties of sentences likely to describe interactions between biomolecules. It retrieves sentences containing two terms of interest, and rank them based on their probability to describe interactions between the two given terms. Sentence are clickable links pointing to the original online PubMed citation."
"Zhang L, Berleant D, Ding J, Cao T, Syrkin Wurtele E. PathBinder--text empirics and automatic extraction of biomolecular interactions. BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S18. PubMed PMID: 19811683."
2009
100
PathBLAST
http://www.pathblast.org
"A tool for alignment and comparison of protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The technique discriminates between true- and false-positive interactions and allows for functional annotation of protein interaction pathways based on similarity to the network of another, well-characterized species. The input should specify a short protein interaction path for query against a target PPI network selected from a network database. The output would be a ranked list of matching paths from the target network along with a graphical view of these paths and the overlap among them. Target PPI networks are currently available for Homo sapiens, Mus musculus, Helicobacter pylori, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster species."
"Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8. PubMed PMID: 15215356; PubMed Central PMCID: PMC441549."
2004
100
PathBuilder - Pathway Annotation Tool
http://pathbuilder.sourceforge.net
"A software for annotating biological information related to signaling pathways and to create web-based pathway resources. It enables annotation of molecular events such as PPIs, enzyme-substrate relationships and protein translocation events either manually or through automated importing of data from other databases. The features include automatic validation of data formats, built-in modules for visualizing pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving pathway datasets."
"Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A. PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics. 2009 Nov 1;25(21):2860-2. Epub 2009 Jul 23. PubMed PMID: 19628504; PubMed Central PMCID: PMC2781757."
2009
100
Pathway Studio
http://www.ariadnegenomics.com/products/pathway-studio
"Gene expression or proteomics data analysis software that helps to: build, expand and analyze pathways; find relationships among genes, proteins, cell processes and diseases; draw publication-quality pathway diagrams. The application is useful in navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It finds common regulators and associates pathway components. Pathway Studio supports the Prolexys HyNet protein-protein interaction database. It can also import data from various databases such as Gene Ontology, HPRD, GEO."
"Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio--the analysis and navigation of molecular networks. Bioinformatics. 2003 Nov 1;19(16):2155-7. PubMed PMID: 14594725."
2003
100
PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition
http://www.patika.org
"A database that integrates data from several sources, including Entrez Gene, UniProt, PubChem, Gene Ontology, IntAct, HPRD, and Reactome. Currently focuses only on human pathway data and currently contains several thousand states of many different biological entities and a few thousand reactions. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. "
"Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics. 2002 Jul;18(7):996-1003. PubMed PMID: 12117798."
2002
100
PBEQ-Solver
http://www.charmm-gui.org/input/pbeqsolver
"A web-based tool to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. It calculates the electrostatic potential and solvation free energy, protein-protein (DNA or RNA) electrostatic interaction energy and pKa of a selected titratable residue. "
"Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W270-5. Epub 2008 May 28. PubMed PMID: 18508808; PubMed Central PMCID: PMC2447802."
2008
100
PCFamily - Protein Complex Family Search
http://pcfamily.life.nctu.edu.tw
"A web-based server that identifies template-based homologous protein complexes (PCF) and infers functional modules of the query proteins. PCFamily can provide involved complex family analysis, interface composition, evolution analysis for the query. Input is a PDB code or protein sequence (single/multiple). Based on homologous complexes across multiple species, the sever infers binding models, functional modules, and the conserved interacting domains and Gene Ontology annotations of the PCF."
"Lo YS, Lin CY, Yang JM. PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W516-22. Epub 2010 May 28. PubMed PMID: 20511590; PubMed Central PMCID: PMC2896147."
2010
100
PDbase
http://bioportal.kobic.re.kr/PDbase
"A database of Parkinson's disease (PD)-related gene and genetic variations using the substantia nigra (SN) PD and normal tissues and integrated PD-related information from several resources including protein-protein interactions. Contains PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. It provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms markers within PD-related gene structures, repeat elements, and pathways and networks with PPI information."
"Yang JO, Kim WY, Jeong SY, Oh JH, Jho S, Bhak J, Kim NS. PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. BMC Genomics. 2009 Dec 3;10 Suppl 3:S32. PubMed PMID: 19958497; PubMed Central PMCID: PMC2788386."
2009
100
PDBSite
http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite
"A resource that provides comprehensive structural and functional information on various protein sites including post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions, in PDB. It contains functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. Database can be queried through the functional description and structural characteristics of the site and its environment."
"Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA. PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D183-7. PubMed PMID: 15608173; PubMed Central PMCID: PMC540059."
2005
100
PDBSiteScan
http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html
"A tool for searching active, binding and posttranslational modification sites in the 3D structures of proteins. Tool is set up by automated processing of the PDB database and PPI sites were generated by analysis of atom coordinates in heterocomplexes."
"Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W549-54. PubMed PMID: 15215447; PubMed Central PMCID: PMC441577."
2004
100
PDZBase
http://icb.med.cornell.edu/services/pdz
A resource specific to PDZ domain mediated interactions.
"Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics. 2005 Mar;21(6):827-8. Epub 2004 Oct 28. PubMed PMID: 15513994."
2004
100
PEDANT - Protein Extraction, Description and ANalysis Tool
http://pedant.gsf.de
"A resource that provides an exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools. It features a set of tools for genome comparison, protein function prediction based on genomic context, computation and visualization of PPI networks based on experimental data, etc."
"Frishman D, Mokrejs M, Kosykh D, Kastenmüller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K, Mewes HW. The PEDANT genome database. Nucleic Acids Res. 2003 Jan 1;31(1):207-11. PubMed PMID: 12519983; PubMed Central PMCID: PMC165452."
2003
100
PepCrawler
http://bioinfo3d.cs.tau.ac.il/PepCrawler
A tool for prediction of peptide-protein complexes and deriving binding peptides from protein-protein complexes by performing high-resolution docking refinement and estimation of binding affinity. Input is a complex PDB file (either protein-protein or protein-peptide).
"Donsky E, Wolfson HJ. PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors. Bioinformatics. 2011 Oct 15;27(20):2836-42. Epub 2011 Aug 31. PubMed PMID: 21880702."
2011
100
PepCyber: P~Pep
http://www.pepcyber.org/PPEP
"A database of human PPIs mediated by phosphoprotein-binding domains (PPBD). It contains experimentally validated data for PPBD interactions. Interaction network can be viewed in a graphical format and can be downloaded in various other formats. Database can be queried with PPBD protein or class, interactions."
"Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T. PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Res. 2008 Jan;36(Database issue):D679-83. Epub 2007 Dec 26. PubMed PMID: 18160410; PubMed Central PMCID: PMC2238930."
2008
100
PepDist
http://www.pepdist.cs.huji.ac.il
A server that predicts protein-peptide interactions. It predicts the binding affinity to a number of different MHC class I alleles using peptide-peptide distance functions.
"Chen Yanover and Tomer Hertz. Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. In Lecture Notes in Computer Science, Volume 3500, Pages 456-471."
2005
100
PhosphoPOINT - a comprehensive human interactome and phosphoprotein database
http://kinase.bioinformatics.tw
"A database of human kinase interactome and phospho-proteins. It annotates the interactions among kinases, and modulate the kinase-substrate pairs. It implements various gene expression profiles and Gene Ontology cellular component information to evaluate kinases and their interacting phospho-proteins/substrates."
"Yang CY, Chang CH, Yu YL, Lin TC, Lee SA, Yen CC, Yang JM, Lai JM, Hong YR, Tseng TL, Chao KM, Huang CY. PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics. 2008 Aug 15;24(16):i14-20. PubMed PMID: 18689816."
2008
100
PIANA - Protein Interactions And Network Analysis
http://sbi.imim.es/piana
"A software that helps in performing analyses of protein interaction networks, integrating many interaction repositories into a single network, predicitng new interactions, finding interaction distance between the proteins, clustering the interaction networks based on Gene Ontology terms. It can also give the pathway related to PPI network. Protein interaction network data in PIANA is extracted from databases: DIP, MIPS, HPRD, BioGRID, IntAct, MINT, BIND and STRING. Also uses the interactions specified by the user via simple flat text files."
"Aragues R, Jaeggi D, Oliva B. PIANA: protein interactions and network analysis. Bioinformatics. 2006 Apr 15;22(8):1015-7. Epub 2006 Mar 1. PubMed PMID: 16510498."
2006
100
PIBASE - a database of structurally defined protein interfaces
http://salilab.org/pibase
"Database of protein structural interfaces derieved from the PDB and PQS databases. Composed of binary interfaces extracted from structures, using domain assignments from the Structural Classification of Proteins and CATH fold classification systems."
"Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics. 2005 May 1;21(9):1901-7. Epub 2005 Jan 18. PubMed PMID: 15657096."
2005
100
PIC - Protein Interactions Calculator
http://pic.mbu.iisc.ernet.in
"A platform that computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex, for a given coordinate set of 3D structure of a protein or an assembly. Interactions are calculated based on standard, published criteria. Interactions can be visualized using a RasMol and Jmol interface."
"Tina KG, Bhadra R, Srinivasan N. PIC: Protein Interactions Calculator. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W473-6. Epub 2007 Jun 21. PubMed PMID: 17584791; PubMed Central PMCID: PMC1933215."
2007
100
PICCOLO
http://www-cryst.bioc.cam.ac.uk/piccolo
"A database that gprovides atomic-level characterization of structurally characterized PPIs. It describes the interactions at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Input is a PDB code."
"Bickerton GR, Higueruelo AP, Blundell TL. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. BMC Bioinformatics. 2011 Jul 29;12:313. PubMed PMID: 21801404; PubMed Central PMCID: PMC3161047."
2011
100
PICorpus - Protein Interaction Corpus
http://bionlp-corpora.sourceforge.net/picorpus
"A software that can be used for a variety of biomedical language processing tasks, including testing entity extraction, relation identification and relation extraction systems. "
"Johnson HL, Baumgartner WA Jr, Krallinger M, Cohen KB, Hunter L. Corpus refactoring: a feasibility study. J Biomed Discov Collab. 2007 Sep 13;2:4. PubMed PMID: 17854502; PubMed Central PMCID: PMC2072937."
2007
100
PID - Pathway Interaction Database
http://pid.nci.nih.gov
"A database that provides a highly structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is focused on the biomolecular interactions that are known or believed to take place in human cells. PID has three types of data: NCI (Nature Cancer Institute)-Nature Curated data, created by Nature Publishing Group editors and reviewed by experts in the field; data from BioCarta; and human pathways data form Reactome. Analysis of larger gene-sets such as obtaining interaction network maps for all biomolecules in your list or overlay your biomolecules onto predefined pathway(s) can be performed by using batch query option."
"Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. Epub 2008 Oct 2. PubMed PMID: 18832364; PubMed Central PMCID: PMC2686461."
2008
100
PIE - Protein Interaction information Extraction system
http://pie.snu.ac.kr
"Protein-protein interaction extraction system, that extracts PPIs from literature or for the given text/sentences. Input can be a PMID, PDF file, user defined text. The system utilizes natural language processing techniques and machine learning methodologies to predict PPI sentences."
"Kim S, Shin SY, Lee IH, Kim SJ, Sriram R, Zhang BT. PIE: an online prediction system for protein-protein interactions from text. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W411-5. Epub 2008 May 28. PubMed PMID: 18508809; PubMed Central PMCID: PMC2447724."
2008
100
PIG - Pathogen Interaction Gateway
http://pig.vbi.vt.edu
A database of host-pathogen PPIs. It collects and integrates data from a number of public resources. Provides a number of user interfaces for searching data and tools for predicting interactions.
"Driscoll T, Dyer MD, Murali TM, Sobral BW. PIG--the pathogen interaction gateway. Nucleic Acids Res. 2009 Jan;37(Database issue):D647-50. Epub 2008 Nov 4. PubMed PMID: 18984614; PubMed Central PMCID: PMC2686532."
2008
100
PIMRider
http://pim.hybrigenics.com
"A web-resource to explore of protein pathways. Features include graphical exploration of protein-interaction maps, interaction scoring method, details on interactions including selected interaction domains, integration of a curated genomic database for each organism studied. "
Not available
Not available
100
PIMWalker
https://pim.hybrigenics.com/pimriderext/pimwalker
"Tool for the visualization of protein interaction networks, described in a file using the Proteomics Standards Initiative-Molecular Interaction (PSI-MI) format."
"Meil A, Durand P, Wojcik J. PIMWalker: visualising protein interaction networks using the HUPO PSI molecular interaction format. Appl Bioinformatics. 2005;4(2):137-9. PubMed PMID: 16128615."
2005
100
PINA - Protein Interaction Network Analysis
http://cbg.garvan.unsw.edu.au/pina
"A web-based platform for analyzing PPIs. Th platform integrates PPI data from six databases and provides network construction, filtering, analysis and visualization tools. Currently has non-redundant protein interaction dataset for six model organisms. Network analysis include topology, function and common interactions. Interactions can be filtered by annotations and GO similarity. User can also identify enriched modules in the list of query proteins against the background. Query can be a single/list of proteins/list of interactions. "
"Wu J, Vallenius T, Ovaska K, Westermarck J, Mäkelä TP, Hautaniemi S. Integrated network analysis platform for protein-protein interactions. Nat Methods. 2009 Jan;6(1):75-7. Epub 2008 Dec 14. PubMed PMID: 19079255."
2008
100
PINAT - Protein Interaction Network Analysis Tool
www.manit.ac.in/pinat
A protein interaction network analysis tool that identifies potential protein interaction for drug target identification. It helps in network building by using co-evolutionary profile. It provides facilities for the assembly of data for network building with visual presentation of the results and interaction score.
"Kushwaha SK, Shakya M. PINAT1.0: protein interaction network analysis tool. Bioinformation. 2009 Jul 27;3(10):419-21. PubMed PMID: 19759862; PubMed Central PMCID: PMC2737494."
2009
100
PiNAT - Protein interaction Network Assessment Tool
https://rostlab.org/owiki/index.php/PiNAT
"A protein interaction network analysis and assessment tool, that analyzes the networks and simulates the flow of processes and pathways in the cell. The user input list of protein identifiers are queried for experimentally known interactions in various PPI databases. It integrates information regarding protein function and sub-cellular localization and gives the reliable interactions involving the query proteins. Also predicts the localization of the interactions. User network can also be imported for analysis."
"Ofran Y, Yachdav G, Mozes E, Soong TT, Nair R, Rost B. Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics. 2006 Jul 15;22(14):e402-7. PubMed PMID: 16873500."
2006
100
PINdb - Proteins Interacting in the Nucleus database
http://pin.mskcc.org
A database specific to human and yeast species. Provides nucleus specific interactions and complexes.
"Luc PV, Tempst P. PINdb: a database of nuclear protein complexes from human and yeast. Bioinformatics. 2004 Jun 12;20(9):1413 5. Epub 2004 Apr 15. PubMed PMID: 15087322."
2004
100
PINT - Protein-protein Interactions Thermodynamic
http://www.bioinfodatabase.com/pint
A resource that provides the kinetics/thermodynamics of the interactions. Considers only PubMed for retrieving PPIs. Provides options for uploading or submitting the interaction data.
"Kumar MD, Gromiha MM. PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D195-8. PubMed PMID: 16381844"
2006
100
PIP - Potential Interactions of Proteins
bmm.cancerresearchuk.org/~pip
"A web-server for potential PPIs of human, rat and fission yeast proteins. Interaction predictions are derived from homology with experimentally known PPIs from various species. It searches for homologues to proteins that have been found experimentally to interact. Also gives a confidence score for the interactions predicted. Protein interaction graphs in PIP are created by the Graphviz software."
"Jonsson PF, Cavanna T, Zicha D, Bates PA. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics. 2006 Jan 6;7:2. PubMed PMID: 16398927; PubMed Central PMCID: PMC1363365."
2006
100
PIPE - Protein-Protein Interaction Prediction Engine
http://cgmlab.carleton.ca/PIPE2
A PPI prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. It predicts PPIs for any target pair of the yeast Saccharomyces cerevisiae proteins based on their primary structure. It can also be used to analyze the internal architecture of yeast protein complexes. User can set the specificity and sensitivity of the interaction.
"Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics. 2006 Jul 27;7:365. PubMed PMID: 16872538; PubMed Central PMCID: PMC1557541."
2006
100
PIPs - Human Protein-Protein Interaction Prediction
http://www.compbio.dundee.ac.uk/www-pips
"A database specific to human PPIs. Predicts interaction based on co-expression, domain/interfaces/sites, co-localization and co-occurrence of PTMs."
"McDowall MD, Scott MS, Barton GJ. PIPs: human protein-protein interaction prediction database. Nucleic Acids Res. 2009 Jan;37(Database issue):D651-6. Epub 2008 Nov 6. PubMed PMID: 18988626; PubMed Central PMCID: PMC2686497."
2008
100
PIPSA - Protein Interaction Property Similarity Analysis
http://projects.villa-bosch.de/mcmsoft/pipsa/3.0
A tool that computes and analyzes the pairwise similarity of 3D interaction property fields for a set of proteins.
"Blomberg N, Gabdoulline RR, Nilges M, Wade RC. Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. Proteins. 1999 Nov 15;37(3):379-87. PubMed PMID: 10591098."
1999
100
PiSITE - Database of Protein interaction SITEs
http://pisite.hgc.jp
"A database of PPI sites. Gives information of interaction sites of a protein from multiple PDB entries including similar proteins, in addition to information from single PDB entry."
"Higurashi M, Ishida T, Kinoshita K. PiSite: a database of protein interaction sites using multiple binding states in the PDB. Nucleic Acids Res. 2009 Jan;37(Database issue):D360-4. Epub 2008 Oct 4. PubMed PMID: 18836195; PubMed Central PMCID: PMC2686547."
2008
100
pISTil - Pipeline for Interaction Sequence Tag identification and analysis
http://pbildb1.univ-lyon1.fr/pistil
A tool for analysis for experimental protein interaction data-sets. The web-interface facilitates to establish a standardised system to analyse and to annotate interaction sequence tags generated by two-hybrid technologies with high performance and flexibility and to provide high-quality PPI datasets.
"Pellet J, Meyniel L, Vidalain PO, de Chassey B, Tafforeau L, Lotteau V, Rabourdin-Combe C, Navratil V. pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis. BMC Res Notes. 2009 Oct 29;2:220. PubMed PMID: 19874608; PubMed Central PMCID: PMC2776022."
2009
100
PLAN2L - Plant annotation to literature
http://zope.bioinfo.cnio.es/plan2l
"A web-based tool for integrated text mining and literature-derived bio-entity relation extraction. The system incorporates information extraction of individual entities including retrieval of protein interaction relations and gene regulatory associations, ranking them according to their relevance for central developmental processes studied in higher plants, namely flowering, leaf, root and seed development. PLAN2L also integrates a localization retrieval module for finding location evidence descriptions. A supervised machine learning-based sentence classifier has been used to score each protein co-occurence sentences and predict protein interactions. Queries include gene/proteins, keywords and pairs of bio-entities. "
"Krallinger M, Rodriguez-Penagos C, Tendulkar A, Valencia A. PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W160-5. Epub 2009 Jun 11. PubMed PMID: 19520768; PubMed Central PMCID: PMC2703909."
2009
100
Plasmod-PPI/PPPI - Plasmodium Protein-Protein Interactions
http://miaja.tic.udc.es/Bio-AIMS/PlasmodPPI.php
A database specific to Plasmodium PPIs.
"Yamilet Rodriguez-Soca, Cristian R. Munteanu, Julian Dorado, Juan Rabuñal, Alejandro Pazos and Humberto González-Díaz, Plasmod-PPI: a web-server predicting complex biopolymer targets in Plasmodium with entropy measures of protein-protein interactions, Polymer 51(1), 264-273 (2010)"
2010
100
PlateletWeb | Interactome
http://plateletweb.bioapps.biozentrum.uni-wuerzburg.de
"A database for human platelet proteins and interactions. It covers the human platelet proteome, transcriptome and interactome. Interactions are derived by mapping platelet-specific expression data (SAGE or proteome) to literature-curated data from HPRD and yeast two hybrid. It also gives information on ncludes key domains, protein Gene Ontology annotations, and receptors."
"Dittrich M, Birschmann I, Mietner S, Sickmann A, Walter U, Dandekar T. Platelet protein interactions: map, signaling components, and phosphorylation groundstate. Arterioscler Thromb Vasc Biol. 2008 Jul;28(7):1326-31. Epub 2008 May 1. PubMed PMID: 18451328."
2008
100
PluriNetWork - Pluripotency associated Network
http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork
A software to explore manually curated protein/gene interaction and regulation network describing pluripotency in mouse.
"Som A, Harder C, Greber B, Siatkowski M, Paudel Y, Warsow G, Cap C, Schöler H, Fuellen G. The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PLoS One. 2010 Dec 10;5(12):e15165. PubMed PMID: 21179244; PubMed Central PMCID: PMC3003487."
2010
100
PML network - a manually curated network of PML nuclear body interactions
http://www.ua.ac.be/ppse
"A manually curated network of the promyelocytic nuclear body interactome. Interaction network is established in Cytoscape, by integration of promyelocytic protein interaction data retrieved from databases and literature."
"Van Damme E, Laukens K, Dang TH, Van Ostade X. A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int J Biol Sci. 2010 Jan 12;6(1):51-67. Review. PubMed PMID: 20087442; PubMed Central PMCID: PMC2808052."
2010
100
POINeT
http://poinet.bioinformatics.tw
"A web-server for PPI searching, analysis, and visualization. It merges PPI and tissue-specific expression data from multiple resources. Many filtering options such as shared Gene Ontology terms, interaction type, interaction in same species, iterations, literature support are available."
"Lee SA, Chan CH, Chen TC, Yang CY, Huang KC, Tsai CH, Lai JM, Wang FS, Kao CY, Huang CY. POINeT: protein interactome with sub-network analysis and hub prioritization. BMC Bioinformatics. 2009 Apr 21;10:114. PubMed PMID: 19379523; PubMed Central PMCID: PMC2683814."
2009
100
POINT - Prediction of interactome database
http://point.bioinformatics.tw
"A database for the prediction of the human protein-protein interactions based on available orthologous interaction datasets. It integrates mouse, fruit fly, worm and yeast PPIs datasets from several publicly accessible databases. The database also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology derive the likelihood of biological relevance of each predicted interacting sets of protein partners."
"Huang TW, Tien AC, Huang WS, Lee YC, Peng CL, Tseng HH, Kao CY, Huang CY. POINT: a database for the prediction of protein protein interactions based on the orthologous interactome. Bioinformatics. 2004 Nov 22;20(17):3273-6. Epub 2004 Jun 24. PubMed PMID: 15217821."
2004
100
POLAR MAPPER - polar maps of protein interaction networks
http://kdbio.inesc-id.pt/software/polarmapper
A software for integrated visualization of protein interaction networks and mRNA expression data. It facilitates the analysis of mRNA expression data in the context of the underlying protein interaction network. It helps in exposing the architecture of protein interaction networks.
"Gonçalves JP, Grãos M, Valente AX. POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. J R Soc Interface. 2009 Oct 6;6(39):881-96. Epub 2008 Nov 28. PubMed PMID: 19091689; PubMed Central PMCID: PMC2684442."
2009
100
PolySearch
http://wishart.biology.ualberta.ca/polysearch
"A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. The typical queries supported by PolySearch are diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. The tool highlights and rank informative abstracts, paragraphs or sentences. Results can be filtered based on z-score and relevancy."
"Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. Epub 2008 May 16. PubMed PMID: 18487273; PubMed Central PMCID: PMC2447794."
2008
100
POLYVIEW-3D - Versatile annotation and high quality visualization of macromolecular structures
http://polyview.cchmc.org/polyview3d.html
"A tool for protein structure analysis, with the focus on annotation and visualization of protein complexes. Protein Data Bank entries and the formatted custom files can be submitted to the POLYVIEW server."
"Porollo A, Meller J. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics. 2007 Aug 29;8:316. PubMed PMID: 17727718; PubMed Central PMCID: PMC1978507."
2007
100
POPSCOMP
http://mathbio.nimr.mrc.ac.uk/wiki/POPSCOMP
"An automated tool for analyzing biomolecular complexes. It calculates the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules. It gives information on the residues involved in the complex formation and also estimates the molecular interaction energies. POPSCOMP applies the ""Parameter Optimized Surfaces"" method."
"Kleinjung J, Fraternali F. POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W342-6. PubMed PMID: 15980485; PubMed Central PMCID: PMC1160130."
2005
100
PPI Finder - Human Protein-Protein Interaction Mining Tool
http://liweilab.genetics.ac.cn/tm
"A web-based mining tool for human PPIs. The tool mines the human PPIs from PubMed abstracts based on their co-occurrences and interaction words, followed by evidences in human PPI databases and shared terms in GO database. It can be searched with gene names/IDs or PMID or a pair of gene names/IDs."
"He M, Wang Y, Li W. PPI finder: a mining tool for human protein-protein interactions. PLoS One. 2009;4(2):e4554. Epub 2009 Feb 23. PubMed PMID: 19234603; PubMed Central PMCID: PMC2641004."
2009
100
PPI spider
http://www.bioprofiling.de/PPI_spider.html
A web-based tool to analyze gene/protein list using as reference knowledge a global PPI network from IntAct database. The method infers a network model from an experimentally identified protein list based on the available information about the topology of the global PPI network.
"Antonov AV, Dietmann S, Rodchenkov I, Mewes HW. PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks. Proteomics. 2009 May;9(10):2740-9. PubMed PMID: 19405022."
2009
100
PPI_SVM
http://code.google.com/p/cmater-bioinfo
A PPI prediction method that predicts interactions between two protein sequences by exploiting their domain information.
"Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D. PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables. Cell Mol Biol Lett. 2011 Jun;16(2):264-78. Epub 2011 Mar 20. PubMed PMID: 21442443."
2011
100
PPID - Protein-Protein Interaction Database
http://www.anc.ed.ac.uk/mscs/PPID
"A manually curated PPI database, focused on human, mouse and rat."
Not available
Not available
100
PPIDD - Protein-Protein Interface Description Database
http://ppidd.cgm.cnrs-gif.fr/ppidd
An extraction and visualisation method of biological protein-protein interfaces from an annotated subset of crystallographic structures of proteins. The tool is focused on the description of protein-protein interfaces corresponding to well-identified classes of protein assemblies.
"Benoit V, Mucchielli-Giorgi MH, Dumont B, Durosay P, Reymond N, Delacroix H. PPIDD: an extraction and visualisation method of biological protein-protein interfaces. Biochimie. 2008 Apr;90(4):640-7. Epub 2007 Nov 28. PubMed PMID: 18086573."
2007
100
PPI-Pred - Protein-Protein Interface Prediction
http://bmbpcu36.leeds.ac.uk/ppi_pred
A tool that analyzes the surface patch and predict protein-protein binding sites. Input is a protein PDB structure and gives an output of most likely binding site location and two other possible locations.
"Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics. 2005 Apr 15;21(8):1487-94. Epub 2004 Dec 21. PubMed PMID: 15613384."
2005
100
PPIRA - Protein-Protein Interactions between Ralstonia solanacearum and Arabidopsis thaliana
http://protein.cau.edu.cn/ppira
A database useful to study plant-pathogen protein interactions. It has predicted PPIs between R. solanacearum and A. thaliana proteins by using two computational methods: the interolog and the domain-based. Input is either R. solancearum or A. thaliana protein name.
"Li ZG, He F, Zhang Z, Peng YL. Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana. Amino Acids. 2011 Jul 24. [Epub ahead of print] PubMed PMID: 21786137."
2011
100
PPISearch - Protein-Protein Interaction Search
http://gemdock.life.nctu.edu.tw/ppisearch
A web-server for searching homologous PPIs across multiple species. It identifies homologous PPIs and infers transferability of interacting domains and functions of a query protein pair. The server also infers the conserved domain-domain pairs (Pfam and InterPro domains) and Gene Ontology annotation pairs. Input is an interacting protein pair to search its homologous interactions across multiple species.
"Chen CC, Lin CY, Lo YS, Yang JM. PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W369-75. Epub 2009 May 5. PubMed PMID: 19417070; PubMed Central PMCID: PMC2703927."
2009
100
ppiTrim - constructing non-redundant and up-to-date interactomes
http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/ppiTrim.html
"A tool for constructing non-redundant and up-to-date PPIs (interactomes). The script processes iRefIndex to produce non-redundant, consistently annotated data sets of physical interactions. It works in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases."
"Stojmirovic A, Yu YK. ppiTrim: constructing non-redundant and up-to-date interactomes. Database (Oxford). 2011 Aug 27;2011:bar036. Print 2011. PubMed PMID: 21873645; PubMed Central PMCID: PMC3162744."
2011
100
PPLook - PPI extraction tool
http://meta.usc.edu/softs/PPLook
"A tool to automatically extract and visualize the PPIs from the text. It also classifies and counts the results by protein type, and display the topological parameters, such as the number of nodes, edges, connected components, etc. It contains modules to: identify if the query word is a protein name or not, pick up sentences containing the query protein name, identify PPI by keywords dictionary pattern-matching by full-sentence parser and visualize PPIs in the form of 3D graph."
"Zhang SW, Li YJ, Xia L, Pan Q. PPLook: an automated data mining tool for protein-protein interaction. BMC Bioinformatics. 2010 Jun 16;11:326. PubMed PMID: 20550717; PubMed Central PMCID: PMC2906489."
2010
100
Predictome
http://predictome.bu.edu
"A database of predicted functional associations among genes and proteins in different organisms. Associations are created using a variety of techniques, both experimental (yeast two-hybrid, immuno-coprecipitation, correlated expression) and computational (gene fusion, chromosomal proximity, gene co-evolution)."
"Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 2002 Jan 1;30(1):306-9. PubMed PMID: 11752322; PubMed Central PMCID: PMC99135."
2002
100
Pred-PPI - Free webserver for predicting protein-protein interactions
http://cic.scu.edu.cn/bioinformatics/predict_ppi
"A web-server for predicting PPIs based on sequence data with probability assignment. Currently for five organisms, specifically humans, yeast, Drosophila, Escherichia coli, and Caenorhabditis elegans. It gives a probability index for the predicted interactions."
"Guo Y, Li M, Pu X, Li G, Guang X, Xiong W, Li J. PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes. 2010 May 26;3:145. PubMed PMID: 20500905; PubMed Central PMCID: PMC2883990."
2010
100
PreSPI - Domain Cohesion and Coupling based PPI prediction
http://code.google.com/p/prespi
A PPI prediction system based on domain combination. It predicts the interaction probability of proteins and develop an interaction possibility ranking method for multiple protein pairs.
"Han DS, Kim HS, Jang WH, Lee SD, Suh JK. PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res. 2004 Dec 1;32(21):6312-20. Print 2004. PubMed PMID: 15576357; PubMed Central PMCID: PMC535680."
2004
100
PRICE - PRotein Interface Conservation and Energetics
http://202.141.148.34/resources/PPI_energetics
"A web-server for the analysis of protein-protein interfaces in the given protein-protein complex. It takes the coordinates of a protein-protein complex, and calculates the degree of conservation and the change in free energy of binding of interface residues. Input is a protein-protein complex structure file."
"Guharoy M, Pal A, Dasgupta M, Chakrabarti P. PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces. J Struct Funct Genomics. 2011 Mar;12(1):33-41. Epub 2011 Apr 26. PubMed PMID: 21519818."
2011
100
PRIME - PRotein Interactions and Molecular Information databasE
http://prime.ontology.ims.u-tokyo.ac.jp:8081
"An integrated gene/protein informatics database based on natural language processing. Provides automatically extracted protein/family/gene/compound interaction information including both physical and genetic interactions, Gene Ontology based functions, and graphic pathway viewers."
"Koike A, Takagi T. PRIME: automatically extracted PRotein Interactions and Molecular Information databasE. In Silico Biol. 2005;5(1):9-20. PubMed PMID: 15972002."
2005
100
PRIN - Predicted Rice Interactome Network
http://bis.zju.edu.cn/prin
"A database to predict the PPIs in Oryza sativa. The prediction method is based on interologs of six model organisms where large-scale PPI experiments have been applied: yeast, worm, fruit fly, human, E.coli and Arabidopsis thaliana. The genome information such as Gene Ontology annotation, subcellular localization information and the gene expression data are added to validate network and get biological significance. Input can be a single or multiple protein IDs."
"Gu H, Zhu P, Jiao Y, Meng Y, Chen M. PRIN: a predicted rice interactome network. BMC Bioinformatics. 2011 May 16;12:161. PubMed PMID: 21575196; PubMed Central PMCID: PMC3118165."
2011
100
PRINCESS - PRotein INteraction Confidence Evaluation System with multple Sources
http://61.50.138.118/picasso
"An online confidence scoring system for evaluating the human high throughput PPIs. It assigns a reliability to the PPI data, based on biological evidences, including model organism PPI, interaction domain, functional annotation, gene expression, genome context, and network topology structure. Input is a protein-interaction list."
"Li D, Liu W, Liu Z, Wang J, Liu Q, Zhu Y, He F. PRINCESS, a protein interaction confidence evaluation system with multiple data sources. Mol Cell Proteomics. 2008 Jun;7(6):1043-52. Epub 2008 Jan 29. PubMed PMID: 18230642."
2008
100
PRODISTIN - Functional classification of proteins based on interactions
http://crfb.univ-mrs.fr/webdistin
"A server for analyzing interaction networks a classification method. It provides a classification tree in which genes/proteins are clustered according to the identity of their interaction partners and functional classes are delineated in the tree using the ""biological process"" Gene Ontology annotations. Input is a list of interactions."
"Brun C, Chevenet F, Martin D, Wojcik J, Guénoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol. 2003;5(1):R6. Epub 2003 Dec 15. PubMed PMID: 14709178; PubMed Central PMCID: PMC395738."
2003
100
PROFEAT - Protein Feature Server
http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi
"A server for computing feature vectors for PPI pairs, single/multiple proteins, small molecule and protein-ligand interactions pairs. User can submit either a single pair of interaction or a list of pair of interactions. It allows to chose from various methods to construct feature vector for PPI pair."
"Li ZR, Lin HH, Han LY, Jiang L, Chen X, Chen YZ. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W32-7. PubMed PMID: 16845018; PubMed Central PMCID: PMC1538821."
2006
100
"A database of protein functional linkages using four methods (phylogenetic profile method, gene cluster method, rosetta stone method and gene neighbour method)."
"Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004;5(5):R35. Epub 2004 Apr 16. PubMed PMID: 15128449; PubMed Central PMCID: PMC416471."
2004
100
PROTCOM - The database of protein complexes
http://www.ces.clemson.edu/compbio/protcom
"A database of protein complexes with a compilation of known 3D structures of protein-protein complexes enriched with artificially created domain-domain structures using the available PDB entries. It allows browsing, searching, visualizing and downloading a pool of protein complexes. It provides an option to select a subset of entries using a combination of up to 10 different criteria."
"Kundrotas PJ, Alexov E. PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 2007 Jan;35(Database issue):D575-9. Epub 2006 Oct 28. PubMed PMID: 17071962; PubMed Central PMCID: PMC1635331."
2006
100
Protein Lounge
www.proteinlounge.com
"A web-site with many interactive web-based databases and software that help in understanding the complexity of systems biology. It has the complete siRNA target database, a complete Peptide-Antigen target database and a Kinase-Phosphatase database. It has the largest database of illustrated signal transduction pathways, which are interconnected to protein database and online gene/protein analysis tools. It has the graphics and animations combining with scientific accuracy to depict PPIs and relevance of proteins in various disease states."
Not available
Not available
100
ProteoConnections
http://www.thibault.iric.ca/proteoconnections
"A platform to facilitate proteome and phosphoproteome data analyses. It organizes the peptide and protein identifications, evaluate the quality of the acquired data-set, profile abundance changes, and accelerate data interpretation. It integrated databases of known PTMs and other bioinformatics tools for various analyses including PPIs. A selected protein dataset can be mapped on the STRING protein interactions network. It gives information on structure, Gene Ontology, PTMs, phosphorylation conservation, domains, etc., for the uploaded data-sets."
"Courcelles M, Lemieux S, Voisin L, Meloche S, Thibault P. ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses. Proteomics. 2011 Jul;11(13):2654-71. doi: 10.1002/pmic.201000776. Epub 2011 May 31. PubMed PMID: 21630457."
2011
100
ProteoLens
http://bio.informatics.iupui.edu/proteolens
"A JAVA-based visual analytic software for creating, annotating and exploring biological networks. It works in two distinct phases: 1) creating network data association rules and attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation."
"Huan T, Sivachenko AY, Harrison SH, Chen JY. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. PubMed PMID: 18793469; PubMed Central PMCID: PMC2537576."
2008
100
Protinfo PPC
http://protinfo.compbio.washington.edu/ppc
"A server that predicts the atomic level structure of a protein complex. For the given protein sequence(s), it searches for homologs in a database of subunit sequences of experimentally determined protein complex structures and builds three dimensional protein complex models for the sequences."
"Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R. Protinfo PPC: a web server for atomic level prediction of protein complexes. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W519-25. Epub 2009 May 6. PubMed PMID: 19420059; PubMed Central PMCID: PMC2703994."
2009
100
Protopia - a Protein-Protein Interaction Tool
http://www.asp.uma.es:8080/Protopia
"A tool that accesses the different protein-interaction databases, and represents in a vector or a matrix. It also compares the results among databases. It also integrates different modules that work together: Graphic User Interface, Model, Visualization Engine, Search Engine Interface, Data Source Adapter Interface and Data Source Extractor Interface."
"Real-Chicharro A, Ruiz-Mostazo I, Navas-Delgado I, Kerzazi A, Chniber O, Sánchez-Jiménez F, Medina MA, Aldana-Montes JF. Protopia: a protein-protein interaction tool. BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S17. PubMed PMID: 19828077; PubMed Central PMCID: PMC2762066."
2009
100
PSIBASE
http://psibase.kobic.re.kr
"A database of molecular interactions that focuses on structural interaction of proteins and their domains. The interactions are predicted based on Prostein Structural Interactome Map (PSIMAP) that is a map of protein interactome. It also provides protein domain assignment module, interaction navigation and visual tools. It can retrieve possible interaction partners for the queried proteins of interest based on significant homology assignments made with their query sequences."
"Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J. PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics. 2005 May 15;21(10):2541-3. Epub 2005 Mar 3. PubMed PMID: 15749693."
2005
100
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks Gateway
http://pstiing.licr.org
"Molecular interactions with ligand-receptor-cell type information and signal transduction modules. Major focus on regulatory networks relevant to chronic inflammation, cell migration and cancer."
"Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M. pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D527-34. PubMed PMID: 16381926; PubMed Central PMCID: PMC1347407."
2006
100
PubNet - Publication Network Graph Utility
http://pubnet.gersteinlab.org
"A web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. It supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, PDB IDs, MeSH terms, and authors."
"Douglas SM, Montelione GT, Gerstein M. PubNet: a flexible system for visualizing literature derived networks. Genome Biol. 2005;6(9):R80. Epub 2005 Aug 16. PubMed PMID: 16168087; PubMed Central PMCID: PMC1242215."
2005
100
PutidaNET
http://sequenceome.kobic.kr/PutidaNET
"A database that provides predicted PPI, Gene Ontology information, and physio-chemical information of Pseudomonas putida KT2440.The serves uses three methods: Protein Structural Interactome MAP (PSIMAP), Protein Experimental Interactome MAP (PEIMAP), and Domain-domain interactions using iPfam, to generate the predictions. It also gives a confidence score for the predictions."
"Park SJ, Choi JS, Kim BC, Jho SW, Ryu JW, Park D, Lee KA, Bhak J, Kim SI. PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. BMC Genomics. 2009 Dec 3;10 Suppl 3:S18. PubMed PMID: 19958481; PubMed Central PMCID: PMC2788370."
2009
100
RAPID - Resource of Asian Primary Immunodeficiency Diseases
http://rapid.rcai.riken.jp
"A web-based resource of molecular alterations in Primary Immunodeficiency Diseases (PID). It provides information on sequence variations and expression at the mRNA and protein levels of all genes reported to be involved in PID patients, along with other relevant information about protein-protein interactions, mouse studies and microarray gene-expression profiles in various organs and cells of the immune system. It also hosts a tool, mutation viewer, that predicts deleterious and novel mutations and also provides mutation-based 3D structures for PID genes."
"Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A, Ohara O, Mohan S. RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Res. 2009 Jan;37(Database issue):D863-7. Epub 2008 Oct 8. PubMed PMID: 18842635; PubMed Central PMCID: PMC2686530."
2008
100
ResNet®
http://www.ariadnegenomics.com/products/resnet
"A database of biological relationships, associations and interactions, extracted from PubMed."
Not available
Not available
100
RINalyzer
http://rinalyzer.de
"A tool to analyze and visualize residue interaction networks (RIN). Interaction networks are constructed from the 3D structure of a protein. It allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, together with the corresponding molecular 3D structure visualized in UCSF Chimera. The tool is complemented by the RINerator module, which generates user-defined RINs from a 3D protein structure."
"Doncheva NT, Klein K, Domingues FS, Albrecht M. Analyzing and visualizing residue networks of protein structures. Trends Biochem Sci. 2011 Apr;36(4):179-82. Epub 2011 Feb 21. PubMed PMID: 21345680."
2011
100
SCOPPI - Structural Classification of Protein-Protein Interfaces
http://www.scoppi.org
"Provides domain interactions and their interfaces, derived from PDB and SCOP databases."
"Winter C, Henschel A, Kim WK, Schroeder M. SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D310-4. PubMed PMID: 16381874; PubMed Central PMCID: PMC1347461."
2006
100
SCOWLP - Structural Characterization Of Water, Ligands and Proteins
http://www.scowlp.org
"A web-server for comparative analysis of protein interactions and structural classification of protein binding regions at protein family level, based on the information obtained from high-resolution 3D protein-protein and protein-peptide complexes. Comparisons can be performed at atomic level that allows the user to study interactome conservation and variability. Also includes protein-nucleic acid and protein-saccharide interactions. "
"Teyra J, Doms A, Schroeder M, Pisabarro MT. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics. 2006 Mar 2;7:104. PubMed PMID: 16512892; PubMed Central PMCID: PMC1459204."
2006
100
SHARP2 - A server for the prediction of protein interaction sites on the surface of protein structures
http://www.bioinformatics.sussex.ac.uk/SHARP2
"A web-based tool for predicting potential PPI sites on protein structures, based on predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. It includes 6 parameters: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion."
"Murakami Y, Jones S. SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics. 2006 Jul 15;22(14):1794-5. Epub 2006 May 3. PubMed PMID: 16672257."
2006
100
SNAPPI - Structures, iNterfaces and Alignments of Protein-Protein Interactions
www.compbio.dundee.ac.uk/SNAPPI
"A database of structures, interfaces and alignments of PPIs. The SNAPPI-Package consists of SNAPPI-DB, SNAPPI-View and SNAPPI-Predict. It provides domain-domain interactions observed in structural data. Also includes associated SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, protein quaternary structures and secondary structure information."
"Jefferson ER, Walsh TP, Roberts TJ, Barton GJ. SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res. 2007 Jan;35(Database issue):D580-9. PubMed PMID: 17202171; PubMed Central PMCID: PMC1899103."
2007
100
SNAVI - Signaling Networks Analysis and Visualization
http://code.google.com/p/snavi
"A desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. It generates linked web pages from network datasets loaded in text format.It also create networks from lists of gene or protein names."
"Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R. SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst Biol. 2009 Jan 20;3:10. PubMed PMID: 19154595; PubMed Central PMCID: PMC2637233."
2009
100
SNOW - Studying Networks in the OMIC World
http://babelomics.bioinfo.cipf.es/snow.html
"A web-based tool for the statistical analysis of PPI networks. It draws the connections among the given list of proteins, calculates several relevant network parameters and, estimates their statistical significance. The parameters include connectivity, betweenness and clustering coefficient. Also calculates the number of components, number of bicomponents and articulation points. The resulting network can be explored by ""interactive network viewer""."
"Minguez P, Götz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W109-14. Epub 2009 May 19. PubMed PMID: 19454602; PubMed Central PMCID: PMC2703972."
2009
100
SPiD
http://genome.jouy.inra.fr/spid
A database specific to Bacillus subtilis PPIs. Provides the interaction sites for a given protein.
"Hoebeke M, Chiapello H, Noirot P, Bessières P. SPiD: a subtilis protein interaction database. Bioinformatics. 2001 Dec;17(12):1209-12. PubMed PMID: 11751229.
2001
100
SPIDer - Saccharomyces protein-protein interaction database
http://cmb.bnu.edu.cn/SPIDer
"A database for predicted Saccharomyces PPIs. Predicted interaction network reconstructed from the gold standard positive datasets. It provides links to connect predicted protein-protein interactions with three other databases, DIP, BIND and MIPS. It provides access to interactions based on various search features including protein information, Gene Ontology term information or sequence similarity. A graphical interface for visualizing an interaction sub-network for a list of proteins of interest is also possible."
"Wu X, Zhu L, Guo J, Fu C, Zhou H, Dong D, Li Z, Zhang DY, Lin K. SPIDer: Saccharomyces protein-protein interaction database. BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S16. PubMed PMID: 17254300; PubMed Central PMCID: PMC1764472."
2006
100
SPPIDER - Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
http://sppider.cchmc.org
"A server to predict residues to be at the putative protein interface(s) by considering single protein chain with resolved 3D structure, analyse protein-protein complex with given 3D structural information and identify residues that are being in interchain contact."
"Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 2007 Feb 15;66(3):630-45. PubMed PMID: 17152079."
2007
100
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
http://string.embl.de
"A database that predicts protein-interactions based on co-expression, genomic data, gene fusion. Also collects PPIs from multiple databases. Provides information on the function of interactions. Can also query with multiple genes/proteins."
"Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000 Sep 15;28(18):3442-4. PubMed PMID: 10982861; PubMed Central PMCID: PMC110752."
2000
100
Struct2Net - Structure-based computational predictions of protein-protein interactions
http://struct2net.csail.mit.edu
"A database specific to human, yeast and Drosophila. Predicts interactions based on the protein structure/structural matching."
"Singh R, Xu J, Berger B. Struct2net: integrating structure into protein-protein interaction prediction. Pac Symp Biocomput. 2006:403-14. PubMed PMID: 17094256.
2006
100
SynechoNET - Integrated protein-protein interaction database of Synechocystis sp. PCC 6803
http://bioportal.kobic.kr/SynechoNET
"An integrated PPI database of a model cyanobacterium Synechocystis sp. PCC 6803. It provides domain-domain interactions, as well as their protein level interactions. Also provides transmembrane topology and domain information, as well as the interaction networks in graphical web interfaces."
"Kim WY, Kang S, Kim BC, Oh J, Cho S, Bhak J, Choi JS. SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. BMC Bioinformatics. 2008;9 Suppl 1:S20. PubMed PMID: 18315852; PubMed Central PMCID: PMC2259421."
2008
100
T1DBase
http://T1DBase.org
"A web-based resource focused on the genetics and genomics of type 1 diabetes susceptibility (T1D). It provides curated and integrated datasets and tools, across multiple species. It includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; functional annotation of genes active in beta cells; ""global"" datasets, generally from the literature, protein interactions, pathways from various resources, Gene Ontology terms, and external links fro many bioinformatic resources."
"Smink LJ, Helton EM, Healy BC, Cavnor CC, Lam AC, Flamez D, Burren OS, Wang Y, Dolman GE, Burdick DB, Everett VH, Glusman G, Laneri D, Rowen L, Schuilenburg H, Walker NM, Mychaleckyj J, Wicker LS, Eizirik DL, Todd JA, Goodman N. T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D544-9. PubMed PMID: 15608258; PubMed Central PMCID: PMC540049."
2005
100
T2D-Db - An integrated Data Resource on Type 2 diabetes
http://t2ddb.ibab.ac.in
"A web-resource, that provides integrated and curated information on almost all known molecular components involved in the pathogenesis of type 2 diabetes mellitus in human, mouse and rat. The information includes candidate genes, SNPs in candidate genes or candidate regions, genome wide association studies, tissue specific gene expression patterns, pathways, PPIs and disease associated risk factors or complications."
"Agrawal S, Dimitrova N, Nathan P, Udayakumar K, Lakshmi SS, Sriram S, Manjusha N, Sengupta U. T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics. 2008 Jul 7;9:320. PubMed PMID: 18605991; PubMed Central PMCID: PMC2491641."
2008
100
T2DM-GeneMiner
http://t2dm-geneminer.molgen.mpg.de
"A web-resource for analysing genes in relation to type 2 diabetes mellitus. It provide access disease relevance for a human or mouse gene. It also includes functional information on cellular networks associated with these genes such as pathway information, PPIs and gene regulatory networks. Can query with gene, transcript or protein."
"Rasche A, Al-Hasani H, Herwig R. Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics. 2008 Jun 30;9:310. PubMed PMID: 18590522; PubMed Central PMCID: PMC2515154."
2008
100
TcoF-DB - Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins
http://apps.sanbi.ac.za/tcof
"A database to explore of proteins involved in the regulation of transcription i.e., transcription factors (TFs), co-factors, and their interactions, in humans. For a queried protein it provides interactions with other TFs, co-factors and TF-binding proteins. Also gives the Gene Ontology terms for the queried protein."
"Schaefer U, Schmeier S, Bajic VB. TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res. 2011 Jan;39(Database issue):D106-10. Epub 2010 Oct 21. PubMed PMID: 20965969; PubMed Central PMCID: PMC3013796."
2010
100
TC-PINs - Time Course Protein Interaction Networks
http://bioinfo.csu.edu.cn/txw/TC-PINs
"An interface ""time course protein interaction networks"" that are reconstructed by incorporating time series gene expression into interaction networks. It creats create functional modules from networks of three types: TC-PINs, a static PPI network and a pseudorandom network. Gene Ontology enrichment analyses are also performed to compare the functional modules."
"Tang X, Wang J, Liu B, Li M, Chen G, Pan Y. A comparison of the functional modules identified from time course and static PPI network data. BMC Bioinformatics. 2011 Aug 15;12:339. PubMed PMID: 21849017; PubMed Central PMCID: PMC3174950."
2011
100
TopNet - Topology of Networks
http://networks.gersteinlab.org/genome/interactions/networks/core.html
An automated web tool that calculates and compares topological characteristics for different sub-networks derived from any given protein network.
"Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res. 2004 Jan 14;32(1):328-37. Print 2004. PubMed PMID: 14724320; PubMed Central PMCID: PMC373274."
2004
100
ToppGene Suite
http://toppgene.cchmc.org
"A web-resource for gene list functional enrichment, candidate gene prioritization using either functional annotations or network analysis, and identification and prioritization of novel disease candidate genes in the interactome. It integrated several tools for the functional analysis of the genes such as ToppFun, for functional enrichment; ToppGene, for candidate gene prioritization; ToppNet, for finding importance of candidate genes in networks and ToppGenet, for prioritization of neighboring genes in PPI network."
"Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11. Epub 2009 May 22. PubMed PMID: 19465376; PubMed Central PMCID: PMC2703978."
2009
100
TORQUE - topology-free querying of protein interaction networks
http://www.cs.tau.ac.il/~bnet/torque.html
"A tool for cross-species querying of PPI networks, that seeks a matching set of proteins that are sequence similar to the query proteins and span a connected region of the target network, while allowing for both insertions and deletions."
"Bruckner S, Hüffner F, Karp RM, Shamir R, Sharan R. TORQUE: topology-free querying of protein interaction networks. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W106-8. Epub 2009 Jun 2. PubMed PMID: 19491310; PubMed Central PMCID: PMC2703961."
2009
100
TRANSPATH®
http://www.gene-regulation.com/cgi-bin/pub/databases/transpath
"A database on signal transduction networks. It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Also has tools for visualization and analysis such as ArrayAnalyzer and PathwayBuilder."
"Schacherer F, Choi C, Götze U, Krull M, Pistor S, Wingender E. The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics. 2001 Nov;17(11):1053-7. PubMed PMID: 11724734."
2001
100
TRIP database - TRansient receptor potential channel-Interacting Protein database
http://www.trpchannel.org
A database of curated PPIs for mammalian transient receptor potential channels.
"Shin YC, Shin SY, So I, Kwon D, Jeon JH. TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. Nucleic Acids Res. 2011 Jan;39(Database issue):D356-61. Epub 2010 Sep 17. PubMed PMID: 20851834; PubMed Central PMCID: PMC3013757."
2010
100
Trypano-PPI - Trypanosome Protein-Protein Interactions
http://miaja.tic.udc.es/Bio-AIMS/TrypanoPPI.php
A server that predicts if a pair of proteins form a physically stable complex unique of Trypanosoma (not present in human or other parasites). Prediction is based on electrostatic potential indices of PPIs.
"Rodriguez-Soca Y, Munteanu CR, Dorado J, Pazos A, Prado-Prado FJ, González-Díaz H. Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome by using electrostatic parameters of protein-protein interactions. J Proteome Res. 2010 Feb 5;9(2):1182-90. PubMed PMID: 19947655."
2010
100
TSEMA
http://pdg.cnb.uam.es/TSEMA
A server for prediction of protein pairings between interacting families. The system calculates an initial mapping between two families of proteins and allows the user to interactively modify it based on performance figures and/or specific biological knowledge. Explored mappings are graphically shown over a representation of the phylogenetic trees.
"Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F. TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W315-9. PubMed PMID: 16845017; PubMed Central PMCID: PMC1538787."
2006
100
tYNA - TopNet-like Yale Network Analyzer
http://networks.gersteinlab.org/tyna
"A web-server for managing, comparing and mining multiple networks (biological, computer, social, etc.), both directed and undirected. Network analysis includes identifying defective cliques, finding small network motifs, calculating global statistics, and identifying hubs and bottlenecks. It also has graphical interface."
"Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics. 2006 Dec 1;22(23):2968-70. Epub 2006 Oct 4."
2006
100
Ulysses
http://www.cisreg.ca/ulysses
"A database that predicts human protein interactions based on the homologous interactions in model organisms such as yeast, fly, and worm."
"Kemmer D, Huang Y, Shah SP, Lim J, Brumm J, Yuen MM, Ling J, Xu T, Wasserman WW, Ouellette BF. Ulysses - an application for the projection of molecular interactions across species. Genome Biol. 2005;6(12):R106. Epub 2005 Dec 2. PubMed PMID: 16356269; PubMed Central PMCID: PMC1414088."
2005
100
UniDomInt
http://sonnhammer.sbc.su.se/download/UniDomInt
A database of domain-domain interaction networks. The networks are scored according to the benchmarked reliability of the sources.
"Björkholm P, Sonnhammer EL. Comparative analysis and unification of domain-domain interaction networks. Bioinformatics. 2009 Nov 15;25(22):3020-5. Epub 2009 Aug 31. PubMed PMID: 19720675."
2009
100
UniHI - Unified Human Interactome
http://www.unihi.org
A database to access the integrated available human protein interaction data. The data is collected from major PPI sources.
"Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE, Futschik ME. UniHI: an entry gate to the human protein interactome. Nucleic Acids Res. 2007 Jan;35(Database issue):D590-4. Epub 2006 Dec 7. PubMed PMID: 17158159; PubMed Central PMCID: PMC1781159."
2006
100
VANLO - Visualization of Aligned Networks with Layout Optimization
http://www.math-inf.uni-greifswald.de/VANLO
A system for visualization of aligned biological networks in 3D space that naturally embeds existing 2D layouts. Also provide different interaction techniques to explore the data.
"Brasch S, Linsen L, Fuellen G. VANLO--interactive visual exploration of aligned biological networks. BMC Bioinformatics. 2009 Oct 12;10:327. PubMed PMID: 19821976; PubMed Central PMCID: PMC2766391."
2009
100
VASCo
http://genome.tugraz.at/VASCo
"A visualization tool to calculate and visualize annotated surfaces of proteins with special emphasis on surface contact regions and protein-protein interactions, which are calculated based on surface point distances. The output is most displayed in PyMOL as 'compiled graphics objects' using a custom-made plug-in."
"Steinkellner G, Rader R, Thallinger GG, Kratky C, Gruber K. VASCo: computation and visualization of annotated protein surface contacts. BMC Bioinformatics. 2009 Jan 24;10:32. PubMed PMID: 19166624; PubMed Central PMCID: PMC2649047."
2009
100
VirHostNet
http://pbildb1.univ-lyon1.fr/virhostnet
A database specific to viral-human protein interactions. Provides option for uploading or submitting PPI data.
"Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, André P, Lotteau V, Rabourdin-Combe C. VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D661-8. Epub 2008 Nov 4. PubMed PMID: 18984613; PubMed Central PMCID: PMC2686459.
2008
100
VirusMINT
http://mint.bio.uniroma2.it/virusmint
A database of viral-host protein interactions. Provides option to build interactomes.
"Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, Sacco F, Tinti M, Smolyar A, Castagnoli L, Vidal M, Cusick ME, Cesareni G. VirusMINT: a viral protein interaction database. Nucleic Acids Res. 2009 Jan;37(Database issue):D669-73. Epub 2008 Oct 30. PubMed PMID: 18974184; PubMed Central PMCID: PMC2686573.
2008
100
VisANT - Integrative Visual Analysis Tool for Biological Networks and Pathways
http://visant.bu.edu
"An integrative software platform for the visualization, mining, analysis and modeling of the biological networks. The tool provides: (i) a visual interface for combining and annotating network data, (ii) supporting function and annotation data for different genomes from the Gene Ontology (GO) and KEGG databases and (iii) statistical and analytical tools needed for extracting topological properties of the user-defined networks. The latest version enables visualization, analysis and inference of networks using GO."
"Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5:17. PubMed PMID: 15028117; PubMed Central PMCID: PMC368431."
2004
100
WebInterViewer
http://interviewer.inha.ac.kr
"A database for visualizing and analyzing large-scale molecular interaction networks. It is a web-based version of InterViewer. It finds a layout of the connected components of an entire network, finds a global layout of nodes with respect to pivot nodes within the connected components, refines the local layout of each connected component, it can visualize data directly from protein interaction databases and it provides several abstraction and comparison operations for analyzing large-scale biological networks effectively."
"Han K, Ju BH, Jung H. WebInterViewer: visualizing and analyzing molecular interaction networks. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W89-95. PubMed PMID: 15215357; PubMed Central PMCID: PMC441600."
2004
100
webPIPSA - Protein Interaction Property Similarity Analysis
http://pipsa.eml.org
"A web-server for the comparison of protein interaction properties. It enables the use of Protein Interaction Property Similarity Analysis (PIPSA) to compare and analyze protein electrostatic potentials. It extends and simplifies a PIPSA run. For an input of set of related protein structures in PDB format, it calculates the protein electrostatic potentials, and similarity indices for all pairs of proteins based on the electrostatic similarity."
"Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC. webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W276-80. Epub 2008 Apr 17. PubMed PMID: 18420653; PubMed Central PMCID: PMC2447742."
2008
100
xCOMB
http://phenyx.proteomics.washington.edu/CXDB/index.cgi
A program to compute all possible crosslinks for a given set of proteins. The platform combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files.
"Panchaud A, Singh P, Shaffer SA, Goodlett DR. xComb: a cross-linked peptide database approach to protein-protein interaction analysis. J Proteome Res. 2010 May 7;9(5):2508-15. PubMed PMID: 20302351; PubMed Central PMCID: PMC2884221."
2010
100
XooNET - Integrated protein-protein interaction database of Xanthomonas oryzae pathovar oryzae KACC10331
http://bioportal.kobic.kr/XooNET
"A predicted interactome of Xanthomonas oryzae pathovar oryzae (Xoo). Protein interaction network is predicted by bioinformatics algorithms: Protein Structural Interactome MAP (PSIMAP), Protein Experimental Interactome MAP (PEIMAP) and iPfam. It provides species specific interaction network and host-pathogen interaction. It also provides information on network properties of the Xoo interactome. It shows feasible domain-domain interactions too."
"Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO, Park SJ, Lee BM, Bhak J. Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. BMC Bioinformatics. 2008 Jan 24;9:41. PubMed PMID: 18215330; PubMed Central PMCID: PMC2246157."
2008
100
Yeast KID - Yeast Kinase Interaction Database
http://www.moseslab.csb.utoronto.ca/KID
"A literature curated database for yeast kinases that integrates a series of highthroughput and lowthroughput, genetic, physical, and biochemical experimental evidence with the goal of establishing known kinase-substrate relationships. It provides a ranked score for assessing the quantity and quality of evidence supporting each pair."
"Sharifpoor S, Nguyen Ba AN, Young JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ. A quantitative literature-curated gold standard for kinase-substrate pairs. Genome Biol. 2011;12(4):R39. Epub 2011 Apr 14. PubMed PMID: 21492431; PubMed Central PMCID: PMC3218865."
2011
100
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking
www.yeastract.com
"A curated repository of regulatory associations between Transcription Factors (TFs) and target genes in Saccharomyces cerevisiae, based on bibliographic references. Other related information on TFs such as Gene Ontology annotations is available."
"Stuart GR, Copeland WC, Strand MK. Construction and application of a protein and genetic interaction network (yeast interactome). Nucleic Acids Res. 2009 Apr;37(7):e54. Epub 2009 Mar 9. PubMed PMID: 19273534; PubMed Central PMCID: PMC2673449."
2009
100
YPD - Yeast Proteome Database
http://www.proteome.com/YPDhome.html
A manually curated database from PubMed for yeast proteome. Contains other information related to yeast proteins in additon to interaction.
Garrels JI. YPD-A database for the proteins of Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Jan 1;24(1):46-9. PubMed PMID: 8594598; PubMed Central PMCID: PMC145596.
1996
100
YPPIP - Yeast Protein-Protein Interaction Predictions
http://www.cs.cmu.edu/~qyj/papers_sulp/proteins05_pages/WebService/index.html
"A web-server for predictions on interactions between yeast proteins. Six different classifiers were used to assess the accuracy in predicting interactions, Random Forest (RF), RF similarity-based k-Nearest-Neighbor, Naïve Bayes, Decision Tree, Logistic Regression, and Support Vector Machine. Evidences not only include direct protein interaction but also indirect information such as mRNA expression data, protein-DNA binding data, protein localization data."
"Qi Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins. 2006 May 15;63(3):490-500. PubMed PMID: 16450363."
2006
100
CCSB Interactome Database
http://interactome.dfci.harvard.edu
Provides PPIs for a given gene or set of genes. Includes databases, specific to H. sapiens, C. elegans, S. cerevisiae, A. thaliana, developed by interactome projects at CCSB.
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