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URLs 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
PrePPI A structure-informed database of protein-protein interactions, over 370 000 PPIs for human are considered high confidence Protein-protein analysis (PPI)