PPI databases, network

 

  • PiType - Prediction of protein interaction types based on sequence and network features. PiType does not rely on atomic structures and is thus suitable for characterizing proteome-wide interaction datasets. It can also be used to identify sub-modules within protein complexes - standalone
  • PPI3D - The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures - online
  • Hu-Vir PPI - Molecular principles of human virus protein–protein interactions. Hu-Vir PPI data, DDI and DMI data for human–virus PPI - datasets
  • MI bundle - The MI bundle: enabling network and structural biology in genome visualization tools - standalone
  • IGB - Fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. IGB runs on your desktop and can load data from your local files and also from the internet - database
  • ProPairs - A Data Set for Protein–Protein Docking - datasets
  • Info PPI - Integrated web visualizations for protein-protein interaction databases. Compare databases - database
  • CCMI - Cancer Cell Map Initiative - database
  • HCPIN - Human Cancer Pathway Protein Interaction Network database - database
  • DIMA - A Domain Interaction MAp, it aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains - database and online
  • ProLinks - The ProLinks database is a collection of inferences of functional Linkages between proteins using 4 methods. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional Linkages; the Gene Cluster method, which uses genome proximity to predict functional Linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer Linkage - database
  • Hu-Vir PPI - CCSB binary interactome database - database
  • Structure-PPi - A module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. The Structure-PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein-protein complexes. Structure-PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP, and COSMIC databases - standalone
  • MyProteinNet - Build up-to-date protein interaction networks for organisms, tissues and user-defined contexts (2015) - standalone
  • LMPID - A manually curated database of linear motifs mediating protein-protein interactions - Database
  • structureViz2 - structureViz2: Linking Cytoscape and Chimera - standalone
  • BCL2DB - Database of BCL-2 family members and BH3-only proteins - online
  • InteractoMIX - Combined efforts of Structural Bioinformatics and Bioinsilico labs to deliver a unique web portal to centralize a wide-range of computational tools to exploit interactomics data - online
  • Plant-PrAS - A Database of Physicochemical and Structural Properties and Novel Functional Regions in Plant Proteomes - online
  • APID - Agile Protein Interactomes DataServer is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes - online
  • ComPPI - A cellular compartment-specific database for protein-protein interaction network analysis - online
  • PTMcode v2 - A resource for functional associations of post-translational modifications within and between proteins - .
  • InWeb - The full human interaction network - standalone
  • Mentha - A resource for browsing integrated protein-interaction networks - online
  • Link - ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways - online
  • DAPPLE - DAPPLE stands for Disease Association Protein-Protein Link Evaluator - online
  • FunCoup - The name FunCoup stands for functional coupling. FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms - online
  • NetworkAnalyst - Integrative approaches for protein–protein interaction network analysis and visual exploration - online
  • HybSVM - Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. The web server: automated PB/NPB, SIH/MIH, and date/party prediction is available (predicting protein binding, hub proteins, Predicting structural and kinetic classes for hub proteins) - online
  • POINeT - Protein interactome with sub-network analysis and hub prioritization - .
  • HippDB - A database of readily targeted helical protein-protein interactions - online
  • SippDB - The anatomy of beta-strands at protein-protein interfaces - online
  • PPI Benchmark - Protein docking Benchmark (Univ Massachusetts - UMASS) - .
  • SAPIN - SAPIN: Structural Analysis for Protein Interaction Networks - standalone
  • GUILD - Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization (disease network analysis) - standalone
  • InnateDB - InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection - online
  • DASMIweb - DASMIweb currently has access to 36 distributed data sources. 10 of these provide interaction data that has been experimentally determined or curated from the scientific literature, 24 data sources contain computational predictions, and 2 data sources can be used for scoring the quality of interactions - online
  • Dynactome - The Dynactome Project brings together an international team of scientists to study protein dynamics at a systems level - .
  • CCSB - CCSB Interactome database. (Human Binary Interactome Datasets) - online
  • PINA2 - PINA: Protein Interaction Network Analysis platform. An integrated platform for protein interaction network construction, filtering, analysis, visualization and management (6 databases: IntAct, BioGrid, MINT, DIP, HPRD, MIPS/MPact) - online
  • Jena - The Jena Protein-Protein Interaction Website with many PPI-related databases - online
  • Cytoscape - Cytoscape Web: an interactive web-based network browser - online
  • HitPredict - HitPredict is a resource of high confidence protein-protein interactions. Interactions can be searched and downloaded with their predicted confidence level. Protein-protein interactions from IntAct, BIOGRID and HPRD are combined, annotated and assigned a reliability score in order to identify a high confidence subset - online
  • SPIDer - Saccharomyces Protein-protein Interaction Database - online
  • ProtInDb - ProtInDb is a comprehensive database of protein-protein interface residues extracted from protein complexes in the Protein Data Bank (PDB) - online
  • ComSin - Database of protein structures in bound (Complex) and unbound (Single) states in relation to their intrinsic disorder - online
  • PIBASE - A database of structurally defined protein interfaces - online
  • PIFACE - A clustered protein-protein interface database (clustering protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites, network) - online
  • UniHI - Unified Human Interactome is a database for retrieval, analysis and visualization of human molecular interaction networks. Its primary aim is to provide a comprehensive and easy-to-use platform for network-based investigations to a wide community of researchers in biology and medicine. UniHI 7 currently includes almost 350 000 molecular interactions between genes, proteins and drugs, as well as numerous other types of data such as gene expression and functional annotation - online
  • Pathway Commons - Search and visualize public biological pathway information - Online and Standalone
  • Datasets - Complete Cross Docking Data Of Mintseris Benchmark 2.0 - dataset
  • PATRIC - PATRIC, the bacterial bioinformatics database and analysis resource - online tool
  • EleKit - EleKit allows to measure the similarity of electrostatic potentials between a docked small molecule and a known ligand protein for the same receptor. EleKit is intended to facilitate the design of SMPPIIs (Small Molecule Protein-Protein Interaction Inhibitors) - standalone
  • Udock - Protein-protein cross docking dataset - database
  • PINT - PINT is a Protein-protein Interactions Thermodynamic Database (information about affinity) - database
  • HOMOLOBIND - HOMOLOBIND identifies residues in protein sequences with significant similarity to structurally characterized binding sites - online tool
  • ASEdb - The Alanine Scanning Energetics database - database
  • BISC - BInary SubComplex Database - database
  • PPI Affinity - Protein-Protein Interaction Affinity Database - database
  • HippD - HippD: The database catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface - database
  • HAPPI - Human Annotated and Predicted Protein Interaction - database
  • PIPs - Database of predicted human PPIs - database
  • HPIDB - A unified resource for host-pathogen interactions - database
  • INstruct - A database of high-quality 3D structurally resolved protein interactome networks. Binary interaction data from BioGrid, DIP, HPRD, Intact, MINT, MIPS and VisAnt and domain information from iPfam and 3did were used - database
  • PCDq - Human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset - database
  • NetCAD - A network analysis tool for coronary artery disease-associated PPI network - need to register
  • IRView - A database and viewer for protein interacting regions - database
  • PRIMOS - The Protein Interaction and Molecule Search platform represents a novel web portal that unifies six primary PPI databases (BIND, Biomolecular Interaction Network Database; DIP, Database of Interacting Proteins; HPRD, Human Protein Reference Database; IntAct; MINT, Molecular Interaction Database; and MIPS, Munich Information Center for Protein Sequences) into a single consistent repository. PRIMOS supports three advanced search strategies centering on disease-relevant PPIs, on inter- and intra-organismal crosstalk relations (e.g., pathogen-host interactions), and on highly connected protein nodes analysis (hub identification). The main novelties distinguishing PRIMOS from other secondary PPI databases are the reassessment of known PPIs, and the capacity to validate personal experimental data by our peer-reviewed, homology-based validation - online
  • NetAligner - A network alignment server to compare complexes, pathways and whole interactomes - online
  • Reactome - It is a free, open-source, curated and peer reviewed pathway database - database
  • MPIDB - Microbial protein interaction database - database
  • IMEx - Protein interaction data curation: the International Molecular Exchange (IMEx) consortium - database and more
  • MatrixDB - A database focused on extracellular protein-protein and protein-carbohydrate interactions - database
  • I2D - I2D: Interologous Interaction Database - database
  • NetPro - Molecular Connections, NetPro is a comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references (summer 2013) - database
  • TissueNet - Database of human tissue protein-protein interactions - database online
  • BIND - The Biomolecular Interaction Network Database -  database
  • DIP - Database of interacting proteins -  database, PPI
  • CORUM - The comprehensive resource of mammalian protein complexes - database
  • DOMINE - Database of protein domain interactions - database
  • PepCyber:PPEP - A database of human protein-protein interactions mediated by phosphoprotein-binding domains - database
  • HIPPIE - Human Integrated Protein-Protein Interaction rEference - database
  • BioGRID - The Biological General Repository for Interaction Datasets - database
  • JCB - Numerous information and Links: protein interaction network and databases of complexes can be found at the JCB Protein-Protein Interaction Website - Links and tools for macromolecular interactions
  • PSIbase - A database of Protein Structural Interactome map (PSIMAP) - database
  • PSIbase - Structural Interactome Map of all Proteins - database
  • SCOPPI - A structural classification of protein-protein interfaces - Protein-protein database
  • DOCKGROUND - The resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes - Database of experimental complexes
  • GWIDD - Genome wide docking database, GWIDD is an integrated resource for structural studies of protein-protein interactions on genome-wide scale - online
  • STRING - A database of known and predicted PPI - database
  • PINA - The PINA protein interaction database and Interactome files - database
  • HPRD - Human Protein Reference Database, it 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 - database
  • Drug-SNPing - An integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping All drug-based and protein-protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes - online
  • Interactome3D - A web service for the structural annotation of protein-protein interaction networks - online
  • MINT - The Molecular INTeraction database - online database
  • iRefWeb - A web interface to a broad landscape of data on protein-protein interactions (PPI) - online search for PPI related data
  • Intact - Open source database system and analysis tools for molecular interaction data. As from September 2011, IntAct contains approximately 275000 curated binary interaction evidences from over 5000 publications -  database
  • IMEx - The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort -  database
  • SynSysNet - Based on an expert-curated list of 1.000 human genes, specific to the synapse. Information on resulting proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated - online
  • DOMINO - An open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains - online database
  • SNAPPI - Structures, iNterfaces and Alignments for Protein-Protein Interactions SNAPPI-DB is a database of domain-domain interactions SNAPPI-Predict is a protein-protein interaction prediction program which is currently in development SNAPPI-View is the web interface to SNAPPI-DB and SNAPPI-Predict - online
  • PPISURV - A novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome online PPI - online
  • NETAL - A new graph-based method for global alignment of protein-protein interaction networks - standalone Binaries supported linux
  • PredUs - Prediction of Protein Interfaces Using Structural Alignment - online
  • KBDOCK - 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK integrates protein domain-domain interaction information from 3DID and sequence alignments from PFAM together with structural information from the PDB in order to analyse the spatial arrangements of DDIs by Pfam family, and to propose structural templates for protein docking - Database PPI
  • HotRegion - HotRegion: a database of predicted hot spot clusters - database
  • HINT - High-quality INTeractomes is a database of high-quality protein-protein interactions in different organisms - database
  • PiSITE - Database of Protein interaction SITE - database
  • BioCreAtIvE - Community-wide assessment of text mining methods - .
  • SGI - Second generation structural genomics initiatives focus on protein complexes - .
  • Trypano-PPI - A web server for prediction of unique targets in trypanosome proteome - online
  • Wiki-pi - A web-server of annotated human protein-protein interactions to aid in discovery of protein function - database online
  • SKEMPI - A database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein-protein heterodimeric complexes with experimentally determined structures - database to download
  • SPIN-PP - A database of all protein-protein interfaces present in the PDB - database
  • Link - PPI databases, tools many Links - .
  • SCOWLP - A web-based relational database formed by eleven tables describing PDB interface interactions. The new update also includes 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds - Interfaces - databases online
  • 3did - A collection of domain-domain interaction structures and catalogue of domain-peptide structural motifs in the PDB - online
  • CCDMintseris - Complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information - datasets
  • TissueNet - The TissueNet database of human tissue protein-protein interactions - Protein-protein analysis (PPI), online
  • XLink-DB - Database and Software Tools for Storing and Visualizing Protein Interaction Topology Data - online and the source code can also be found at sourceforge.net
  • PrePPI - A structure-informed database of protein-protein interactions, over 370 000 PPIs for human are considered high confidence - Protein-protein analysis (PPI)
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira