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3DID -- 3D interacting domains
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| Search for domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
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APID -- Agile Protein Interaction DataAnalyzer
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| Search and analyze known experimentally validated protein-protein interactions data.
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APID2NET -- unified interactome graphic analyzer
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| Surf unified interactome data.
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AffinDB -- a freely accessible database of affinities for protein–ligand complexes from the PDB
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| Search for affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank (PDB).
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BindingDB -- a web-accessible database of experimentally determined protein–ligand binding affinities
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| Search for published protein-ligand binding affinity data. |
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BioInfo3D -- A suite of tools for structural bioinformatics
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| Analyze protein structures. |
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CORUM -- the Comprehensive Resource of Mammalian protein complexes
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| Search a collection of experimentally verified mammalian protein complexes.
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CellCircuits -- a database of protein network models
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| Search for information on molecular network models. |
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ClusPro -- An Automated Algorithm for Protein–protein Docking
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| Study protein-protein docking.
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ConsensusPathDB -- a database for integrating human functional interaction networks
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| Find information on metabolic pathways, signal transduction pathways, and gene regulatory networks in humans.
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Cytoprophet -- A Cytoscape plug-in for protein and domain interaction networks inference
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| Infer new potential protein (PPI) and domain (DDI) interactions.
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DDIB - Database of Domain Interactions and Bindings
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| Search for documented information on biomolecule interaction, especially protein domain-domain interactions.
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DIMA 2.0 -- Domain Interaction MAp
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| Database of predicted and known domain interactions.
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DOMINE -- a database of protein domain interactions
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| Database of known and predicted protein domain (domain-domain) interactions.
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DOMINO -- a database of domain–peptide interactions
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| Search for annotated experiments describing interactions mediated by protein-interaction domains.
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Database of Interacting Proteins
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| Find experimentally determined interactions between proteins.
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DePIE -- Designing Primers for Protein Interaction Experiments
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| Design PCR primers for protein-protein interaction experiments. |
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FireDock -- fast interaction refinement in molecular docking
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| Web server for flexible refinement and scoring of protein-protein docking solutions.
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GRAMM-X public web server for protein–protein docking
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| Perform protein docking simulation.
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HIV-1, Human Protein Interaction Database
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| Search for documented interaction of human immunodeficiency virus type 1 (HIV-1) proteins with those of the host cell.
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HOMCOS -- Homology Modeling of Complex Structure
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| Predict interacting protein pairs and interacting sites by homology modeling of complex structures.
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HPID -- Human protein interaction database
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| Search for computed protein-protein interactions in human.
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HotSprint -- Computational Hot Spots of Protein Interfaces
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| Database of computational hot spots in protein interfaces.
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Hubba -- hub objects analyzer
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| A framework of interactome hubs identification for network biology.
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IntAct -- An Open Source Molecular Interaction Database
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| Search and analyze protein interactions.
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Inter-Chain Beta-Sheets -- Protein-protein interactions mediated by interchain beta-sheet formation
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| Search for information on Interchain â-sheet (ICBS) interactions.
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InterDom -- A database of putative interacting protein domains for validating predicted protein interactions and complexes
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| Find evidence for the detected protein interactions based on putative protein domain interactions.
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InterProSurf -- Protein Protein Interaction Server
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| A web server for predicting interacting sites on protein surfaces.
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InterWeaver -- Discovering Potential Protein Interaction Partners with Online Evidence
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| Discover potential protein interactions with online evidence automatically extracted from protein interaction databases, literature abstracts, domain fusion events and domain interactions.
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KDBI -- Kinetic Data of Bio-molecular Interactions database
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| Provides information about experimentally determined kinetics of biomolecular interactions.
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MINT -- Molecular Interactions Database
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| Find functional interactions between biological molecules (proteins, RNA, DNA)
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MPact -- the MIPS protein interaction resource on yeast
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| Access protein-protein interactions resources at MIPS. |
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MiMI -- Michigan Molecular Interactions
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| Retrieve and compare protein interaction data from difference databases.
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NCI -- a server to identify non-canonical interactions in protein structures
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| Identify non-canonical interactions in protein structures.
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NCI/Nature Pathway Interaction Database
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| A collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes.
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NetworkBLAST -- comparative analysis of protein networks
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| Analyzes protein interaction networks across species to infer protein complexes that are conserved in evolution.
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PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
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| Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites. |
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PDBcal -- a comprehensive dataset for receptor-ligand interactions
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| A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry.
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PDZBase -- Protein-protein interactions involving PDZ domains
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| Search for information on protein-protein interaction involving PDZ domains.
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PI2PE -- protein interface/interior prediction engine
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| Protein interface/interior prediction engine.
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PIC -- Protein Interactions Calculator
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| Explore interactions between and within proteins.
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PIG -- the pathogen interaction gateway
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| Find protein-protein interactions in pathogens.
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PINT -- Protein–protein Interactions Thermodynamic Database
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| Search for comprehensive information on protein-protein interaction thermodynamics. |
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PINdb -- a database of nuclear protein complexes from human and yeast
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| Search for documented information on protein complexes purified from the nucleus of human and yeast cells.
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PIPs -- protein-protein interaction prediction database
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| A resource for studying human protein-protein interactions.
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POINT -- a database for the prediction of protein-protein interactions based on the orthologous interactome
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| Predict human protein-protein interactome based on interactome databasets of other model organisms.
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POPSCOMP -- an automated interaction analysis of biomolecular complexes
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| Calculate the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules.
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PRISM -- protein interactions by structural matching
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| Explore protein interfaces and predict protein-protein interactions.
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PROTCOM -- searchable database of protein complexes enhanced with domain-domain structures
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| Search for structural information on protein-protein complexes.
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PathBLAST -- A Tool for Alignment of Protein Interaction Networks
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| Compare protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution.
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PreBI -- prediction of biological interfaces of proteins in crystals
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| Predict biological interfaces in protein crystal structures.
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ProCope -- protein complex prediction and evaluation
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| Access to different methods used for the prediction and evaluation of protein complexes from purification data experiments.
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ProtorP -- A Protein-Protein Interaction Analysis Server
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| Analyze protein-protein associations in 3D structures.
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RosettaDock -- server for local protein-protein docking
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| Predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation.
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SCOPPI -- a structural classification of protein-protein interfaces
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| Search for information on protein domain-domain interfaces and interactions. |
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SNAPPI-DB -- a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions
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| Search for information on structures,interfaces and alignment of protein-protein interactions.
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STRING -- A database of predicted functional associations between proteins
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| Search for information on known and predicted protein-protein interactions.
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SiteEngines -- recognition and comparison of binding sites and protein–protein interfaces
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| Recognize binding sites and interfaces of protein-protein interactions.
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THE DATASET OF PROTEIN-PROTEIN INTERFACES
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| Search for structural information of protein-protein interfaces.
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TSEMA -- interactive prediction of protein pairings between interacting families
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| Predict protein-protein pairing between two interacting protein families based on phylogenetic analysis.
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The Homeodomain Resource
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| Search for curated information for the homeodomain protein family. |
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UniHI -- the Unified Human Interactome database
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| Search for comprehensive information about the human protein interactome.
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VirHostNet -- A database of virus-host interaction networks
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| Find virus-virus, host-host, and virus-host protein interactions.
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VirusMINT -- the Virus Molecular Interaction Database
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| Find interactions between viral and human proteins.
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WebInterViewer -- Visualizing and Analyzing Molecular Interaction Networks
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| Visualize large-scale protein-protein or protein-DNA interactions networks.
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Yeast protein-protein interactions database
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| Find protein-protein interaction for yeast proteins.
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hp-DPI -- Database of protein interactions in Helicobacter pylori
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| Search for documented and predicted protein-protein interaction in Helicobacter pylori.
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iSPOT -- a web tool to infer the interaction specificity of families of protein modules
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| Infer the peptide binding specificity of any member of a family of protein binding domains.
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jSquid -- a Java applet for graphical on-line network exploration
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| A graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks.
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meta-PPISP -- a meta web server for protein-protein interaction site prediction
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| Predict protein-protein interaction sites.
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pSTIING -- a ‘systems’ approach towards integrating signaling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
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| Search for comprehensive knowledge about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis.
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webPIPSA -- Protein Interaction Property Similarity Analysis
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| A web server for the comparison of protein interaction properties.
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