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A comparative account of protein-protein interaction resources, feature-validations and application-based categorizations : Predict PPI network in a species by using ortholog information
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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
100
URL could not be retrieved (20/12/2011).
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
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
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
 
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