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Created on: 23-Oct-2012   Last updated on: 23-Oct-2012  |  How to cite this?
Total resources - 45
A list of resources for protein-nucleic acid interactions
Akhilesh Bajpai and Sravanthi Davuluri (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
TRAP - TRanscription factor Affinity Prediction
http://trap.molgen.mpg.de/cgi-bin/trap_form.cgi
A tool for predicting transcription factor affinities to DNA
1
FlyNets
http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_ page.html  https://www.cistrack.org/flynet 
A database of Drosophila melanogaster molecular interactions including protein-DNA, protein-RNA and protein-protein
50

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
STAP - Sequence To Affinity Prediction
http://biocomp.bioen.uiuc.edu/STAP
A tool to analyze transcription factor-DNA binding data
99

3D-footprint
http://floresta.eead.csic.es/3dfootprint
A database of DNA-binding protein structures, and classification and clusters of protein-DNA interfaces
100
3DinSight
http://gibk26.bio.kyutech.ac.jp/jouhou/3dinsight/3DinSight.html
An integrated database and search tool for structure, property and functional data such as motifs, protein-nucleic acid binding, protein-ligand binding, etc.
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
3DTF - Transcription factor PWMs from 3D structure-based energy calculations
http://cogangs.biobase.de/3dtf
A tool to analyze the protein-DNA binding site and calculate positional weight matrix
100
AANT - Amino Acid-Nucleotide Interaction Database
http://aant.icmb.utexas.edu
A resource of categorized amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures
100
BindN
http://bioinfo.ggc.org/bindn
A tool for efficient prediction of DNA and RNA binding sites in proteins
100
BIPA - Biological Interaction database for Protein-nucleic Acid
http://mordred.bioc.cam.ac.uk/bipa
A database for protein-nucleic acid interactions including various features of protein-nucleic acid interfaces
100
CLIPZ
http://www.clipz.unibas.ch
A tool to analyze binding sites of RNA-binding proteins
100
DDNA3 - DNA-Binding Domain Prediction
http://sparks.informatics.iupui.edu/yueyang/DFIRE/ddna3-DB-service
A tool to predict the protein domain potentially to bind with DNA
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
DNABindR - A Server for Prediction of Protein-DNA interaction sites
http://turing.cs.iastate.edu/PredDNA
A tool for identifying DNA binding residues in protein sequences
100
doRiNA - the BIMSB database of posttranscriptional regulatory elements
http://dorina.mdc-berlin.de/rbp_browser/dorina.html
A database of RNA interactions with binding site data for RNA-binding proteins and miRNAs
100
DP-Bind
http://lcg.rit.albany.edu/dp-bind
A tool for sequence-based prediction of DNA-binding residues in DNA-binding proteins
100
DPInteract
http://arep.med.harvard.edu/dpinteract
A database of DNA-protein interactions
100
dRNA-3D - RNA-binding Protein Prediction from 3D structure
http://sparks.informatics.iupui.edu/yueyang/server/dRNA-DB
A tool for structure-based prediction of RNA-binding domains and RNA-binding sites
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
dRNA-seq - RNA-binding Protein prediction from sequence
http://sparks.informatics.iupui.edu/yueyang/server/dRNA-seq
A tool for prediction of RNA binding proteins by fold recognition and binding affinity prediction
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
DroID - Drosophila Interactions Database
http://www.droidb.org
A database of gene and protein interactions in Drosophila including protein-protein, transcription factor-DNA, miRNA-gene, and genetic interactions
100
EDGEdb - C. elegans differential gene expression database
http://edgedb.umassmed.edu
A database of C. elegans transcription factor-DNA interactions
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
Factorbook
http://factorbook.org
A resource for sequence features and chromatin structure around genomic DNA bound by human transcription factors
100
hPDI - Human Protein-DNA Interactome
http://bioinfo.wilmer.jhu.edu/PDI
A database of human experimental protein-DNA interaction data, identified by protein microarray assays
100
HTHquery - Detecting DNA-binding proteins with a HTH motif
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/HTHquery/index.pl
A tool for detecting DNA-binding proteins with a HTH motif
100
KDBI - Kinetic Data of Biomolecular Interactions
http://bidd.nus.edu.sg/group/kdbi/kdbi.asp
A resource for experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, etc.
100
MatrixREDUCE
http://bussemaker.bio.columbia.edu/software/MatrixREDUCE
A tool for modeling transcription factor-DNA binding domain and analyzing binding affinity
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
NPIDB - Nucleic acid-Protein Interaction DataBase
http://mouse.belozersky.msu.ru/NPIDB
A database, with integrated tools for analyzing DNA-protein and RNA-protein complexes
100
A database of noncoding RNAs and protein related biomacromolecules interactions
100
NUCPLOT
http://www.ebi.ac.uk/thornton-srv/software/NUCPLOT
A tool to generate schematic diagrams of protein-nucleic acid interactions
100
PARalyzer - PAR-CLIP data analyzer
http://www.genome.duke.edu/labs/ohler/research/PARalyzer
A tool for predicting interaction sites between RNA-binding proteins and their targets
100
PDIdb - Protein-DNA Interface Database
http://melolab.org/pdidb
A repository for structural information of protein-DNA complexes solved by X-Ray crystallography
100
PRIDB - Protein-RNA Interface Database
http://pridb.gdcb.iastate.edu
A database for protein-RNA complexes
100
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions
http://gibk26.bio.kyutech.ac.jp/jouhou/pronit/pronit.html
A database for experimentally determined thermodynamic interactions between proteins and nucleic acids
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
ProNuC - Protein-Nucleic Acid Complex Database
http://gibk26.bio.kyutech.ac.jp/jouhou/pronuc/pronuc.html
A resources for structural data of protein-nucleic acid complexes
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
Protein-Nucleic Acid Interaction Server
http://www.biochem.ucl.ac.uk/bsm/DNA/server
A tool for analyzing the protein interface of a protein-nucleic acid complex
100
ProtNA-ASA - Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area
http://www.protna.bio-page.org
A database for known Protein-Nucleic Acid structures and information on accessible surface area of DNA and RNA molecules
100
RBPDB - RNA-Binding Protein DataBase
http://rbpdb.ccbr.utoronto.ca
A database of RNA-binding protein specificities
100
RiceRBP - Rice RNA Binding Protein Database
http://www.bioinformatics2.wsu.edu/cgi-bin/RiceRBP/home.pl
A database and analysis tool of RNA-binding proteins in Oryza sativa
100
RNABindR
http://bindr.gdcb.iastate.edu/RNABindR  http://einstein.cs.iastate.edu/RNABindR 
A server for analyzing and predicting RNA-binding sites in proteins
100

The first URL is not working, as on 15 Nov 2016. Website states that the old version of RNABindR is no longer maintained.
RPISeq - RNA-Protein Interaction Prediction
http://pridb.gdcb.iastate.edu/RPISeq
A tool for predicting RNA-protein interactions
100
RsiteDB - RNA binding sites Data Base
http://bioinfo3d.cs.tau.ac.il/RsiteDB
A database of protein binding pockets that interact with RNA nucleotide bases
100
ScerTF
http://stormo.wustl.edu/ScerTF
A tool to identify all transcription factors that could bind a particular region of DNA sequences if Saccharomyces cerevisiae
100
SpliceAid-F - a database of human splicing factors and their binding sites
http://mi.caspur.it/SpliceAidF
A database of experimentally human RNA-binding splicing regulatory proteins, including relevant information on the RNA binding sites
100

URL not working as on 24 Jan 2014 (confirmed on 15 Nov 2016)
TFinDit - Transcription Factor-DNA Interaction Data Depository
http://bioinfozen.uncc.edu/tfindit
A database of transcription factor-DNA interaction studies
100
tfmodeller
http://maya.ccg.unam.mx/~tfmodell
A resource for protein-DNA complexes and building comparative models of proteins bound to DNA
100
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation
http://the_brain.bwh.harvard.edu/uniprobe
A database for in vitro DNA binding specificities of proteins
100
WebPDA - Web Server of Protein-DNA Complex Structure Analyzer
http://bioinfozen.uncc.edu/webpda
A tool for analyzing protein-DNA complex structures
100
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