Protein Interaction Analysis
Experimental Interactions
The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.
http://mips.gsf.de/proj/ppi/
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
http://www.ebi.ac.uk/intact/site/index.jsf
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.mbi.ucla.edu/
Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the 'MINT Viewer'.
http://mint.bio.uniroma2.it/mint/Welcome.do
Homomint is a web available tool extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens.
http://mint.bio.uniroma2.it/HomoMINT/Welcome.do
The Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies.
http://www.thebiogrid.org/
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform.
http://bioinfow.dep.usal.es/apid/index.htm
Predicted Interactions
STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations.
http://string.embl.de//
Interaction Prediction through Tertiary Structure
web-based tool to predict protein-protein interactions.
http://www.russell.embl.de/cgi-bin/interprets2
I2D ( Interologous Interaction Database) is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks.
http://ophid.utoronto.ca/ophidv2.201/ppi.jsp
Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
http://sppider.cchmc.org
Others
Protein-Protein Interaction Web site at the Jena Center for Bioinformatics
http://www.imb-jena.de/jcb/ppi/
PPI section of the Comprehensive Yeast Genome Database.
http://mips.gsf.de/proj/yeast/CYGD/interaction/
Interactions between HIV and host proteins at the NCBI
http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
A database of protein-protein interactions mediated by interchain ß-sheet formation
http://www.igb.uci.edu/servers/icbs/
A database of protein-protein interactions between large proteins
http://www.kazusa.or.jp/huge/ppi/
Structure 3-D
The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
http://gatealoy.pcb.ub.es/3did/
SNAPPI stands for Structures, iNterfaces and Alignments for Protein-Protein Interactions. The SNAPPI-Package consists of SNAPPI-DB, SNAPPI-View and SNAPPI-Predict.
http://www.compbio.dundee.ac.uk/SNAPPI/index.jsp
This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures.
http://www.ces.clemson.edu/compbio/protcom/
Small Molecules & Peptides
DOMINO: a database of domain-peptide interactions. Many protein interactions are mediated by small protein modules binding to short linear peptides. DOMINO is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains.
http://mint.bio.uniroma2.it/domino/
JenPep is a database of quantitative binding data for immunological protein-peptide interactions.
http://www.jenner.ac.uk/JenPep/
PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains.
http://icb.med.cornell.edu/services/pdz/start
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
http://www.bindingdb.org/bind/index.jsp
SPOT (Sequence Prediction Of Target) is a procedure that is designed to infer the peptide binding specificity of any member of a family of protein binding domains: SH3, PDZ, and WW domains.
http://cbm.bio.uniroma2.it/ispot/
Interactions Nucleic Acid - Proteins
BindN for prediction of DNA and RNA binding residues in proteins
http://bioinfo.ggc.org/bindn/
Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.
http://lcg.rit.albany.edu/dp-bind/
This program predicts the DNA-binding in a protein from their sequence information using neural network.
http://gibk26.bse.kyutech.ac.jp/jouhou/shandar/netasa/dbs-pred/
ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
Various tools and databases on DNA-protein recognition.
http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/recognition.html
Software
Software platform for the visualization of complex interation networks.
http://biodata.mshri.on.ca/osprey/servlet/Index
An integrative platform for network/pathway analysis; visANT = Integrative Visual Analysis Tool for Biological Networks and Pathways.
http://visant.bu.edu/