Protein-protein interaction data | Pathway analysis
Protein function is often modulated by protein-protein interactions (PPIs) and therefore defining the partners of a protein helps to understand its activity. PPIs can be detected through different experimental approaches and are collected in several expert curated databases.…
dbEMT
Data

dbEMT

A literature-based gene resource for exploring epithelial-mesenchymal…

A literature-based gene resource for exploring epithelial-mesenchymal transition (EMT)-related human genes. dbEMT includes literature data, clinical relevant variants, gene expression profiles and…

PCPPI
Data

PCPPI Penicillium-Crop Protein-Protein Interactions database

Is constructed based on the experimentally determined orthologous interactions…

Is constructed based on the experimentally determined orthologous interactions in pathogen-plant systems and available domain-domain interactions (DDIs) in each protein-protein interactions (PPI).…

cisPath
Desktop

cisPath

Uses web browsers to visualize and manage protein-protein interaction (PPI)…

Uses web browsers to visualize and manage protein-protein interaction (PPI) networks. cisPath is an R package that offers functions as a method used to combine the PPI information generated from…

ppiStats
Desktop

ppiStats

Uses for the analysis of protein interaction data. PpiStats is developed as an…

Uses for the analysis of protein interaction data. PpiStats is developed as an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome…

MAPPI-DAT
Desktop
PPI3D
Web

PPI3D

Uses for searching, analyzing and modeling pairwise protein–protein…

Uses for searching, analyzing and modeling pairwise protein–protein interactions (PPI). PPI3D provides both summarized and detailed information on protein interactions in different forms including…

GIANT
Web

GIANT Genome-scale Integrated Analysis of Networks in Tissues

An interface to human tissue networks through multi-gene queries, network…

An interface to human tissue networks through multi-gene queries, network visualization, analysis tools including NetWAS, and downloadable networks. GIANT enables systematic exploration of the…

Schizo-Pi
Web

Schizo-Pi

Predicts protein–protein interactions (PPIs) on hub proteins. Schizo-Pi is…

Predicts protein–protein interactions (PPIs) on hub proteins. Schizo-Pi is based on a random forest model to classify the pairwise features as interacting or non-interacting. This web app would be…

Piface
Data

Piface

Clusters protein-protein interactions (PPI) by their interface structures, and…

Clusters protein-protein interactions (PPI) by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. 22604 unique interfaces, which…

TissueNet
Data

TissueNet

Associates experimentally-identified protein-protein interactions (PPIs) with…

Associates experimentally-identified protein-protein interactions (PPIs) with human tissues. TissueNet allows users to select a protein and a tissue, and to obtain a network view of the query protein…

CORUM
Data

CORUM Comprehensive Resource of Mammalian protein complexes

Provides a resource of manually annotated protein complexes from mammalian…

Provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more.…

AtPID
Data

AtPID Arabidopsis thaliana Protein Interactome Database

Depicts and integrates the information pertaining to protein-protein…

Depicts and integrates the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. AtPID…

BioGRID
Data

BioGRID Biological General Repository for Interaction Datasets

An open access database that houses genetic and protein interactions curated…

An open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID…

DroPNet
Data

DroPNet Drosophila Protein Network

A Drosophila-dedicated web portal for generating and analyzing protein-protein…

A Drosophila-dedicated web portal for generating and analyzing protein-protein interaction (PPI) networks. This platform integrates users' experimental data provided as one or two lists of genes…

FPPI
Data

FPPI F. graminearum Protein-Protein Interaction

Provides comprehensive information of protein-protein interactions (PPIs) of F.…

Provides comprehensive information of protein-protein interactions (PPIs) of F. graminearum predicted based on both interologs from several PPI databases of seven species and domain-domain…

Rintact
Desktop

Rintact

Parses the PSI-25 files generated by the IntAct data repository which collects,…

Parses the PSI-25 files generated by the IntAct data repository which collects, curates and stores thousands of protein interactions. Rintact is an R package which provides two main functions: (i)…

BIOCEMID
Desktop

BIOCEMID BioC Experimental Molecular Interaction Detection

Identifies passages with experimental methods for physical interactions between…

Identifies passages with experimental methods for physical interactions between proteins as an information retrieval search task. BIOCEMID takes a BioC article as input, processes it, and returns the…

MULE
Desktop

MULE Mining Uniquely Labeled Edgesets

Detects conserved interaction patterns in biological networks. MULE uses a…

Detects conserved interaction patterns in biological networks. MULE uses a graph simplification technique based on ortholog contraction, which is ideally suited to biological networks, to render this…

AraPPISite
Data

AraPPISite Arabidopsis Protein-Protein Interaction Site

Provides protein interaction site annotations for plant biologists. Users can…

Provides protein interaction site annotations for plant biologists. Users can query an interested Protein-Protein Interaction (PPI) through either the search page. They also can click each residue in…

PPIM
Data

PPIM Protein-Protein Interraction Database for Maize

Contains both accurately predicted and experimentally verified protein-protein…

Contains both accurately predicted and experimentally verified protein-protein interactions (PPIs). PPIM covers 2,762,560 interactions among 14,000 proteins. It contains not only accurately predicted…

InWeb_IM
Data

InWeb_IM InWeb_InBioMap

A general computational framework that through data integration and quality…

A general computational framework that through data integration and quality control provides a scored human protein-protein interaction network (InWeb_IM). Juxtaposed with five comparable resources,…

TarNet
Data

TarNet

A manually curated database and platform of traditional medicinal plants with…

A manually curated database and platform of traditional medicinal plants with natural compounds that includes potential bio-target information. We gathered information on proteins that are related to…

SPECTRA
Data

SPECTRA SPECific Tissue/Tumor Related PPI networks Analyzer

A framework to build and compare tissue or tumor-specific PPI networks. SPECTRA…

A framework to build and compare tissue or tumor-specific PPI networks. SPECTRA integrates gene expression and protein interaction data from the most authoritative online repositories. SPECTRA…

IntegromeDB
Data

IntegromeDB

A biological web search engine based on the Semantic Web technologies. The…

A biological web search engine based on the Semantic Web technologies. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways,…

PTIR
Data

PTIR Predicted Tomato Interactome Resource

A Predicted Tomato Interactome Resource, based on experimentally determined…

A Predicted Tomato Interactome Resource, based on experimentally determined orthologous interactions in six model organisms. Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626…

A A A
MiasDB
Data

MiasDB

Provides a description of molecular interactions associated with human…

Provides a description of molecular interactions associated with human alternative splicing (AS) events. MiasDB covers 938 interactions between human splicing factors, RNA elements, transcription…

IID
Data

IID Integrated Interactions Database

Provides tissue-specific protein-protein interactions (PPIs) for model…

Provides tissue-specific protein-protein interactions (PPIs) for model organisms and human. IID covers six species and up to 30 tissues per species. Users query IID by providing a set of proteins or…

DESM
Data

DESM

A platform for discovery, analysis and exploration of information from a number…

A platform for discovery, analysis and exploration of information from a number of topic-specific microbial knowledgebases. The knowledgebases include integrated information from published scientific…

SIGNOR
Data

SIGNOR SIGnaling Network Open Resource

Organizes and stores in a structured format signaling information published in…

Organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological…

SInCRe
Data

SInCRe Structural Interactome Computational Resource

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates…

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with…

HPID
Data

HPID Human Protein Interaction Database

It was designed (1) to provide human protein interaction information…

It was designed (1) to provide human protein interaction information pre-computed from existing structural and experimental data, (2) to predict potential interactions between proteins submitted by…

SPIKE
Data

SPIKE Signaling Pathways Integrated Knowledge Engine

A database of highly curated human signaling pathways with an associated…

A database of highly curated human signaling pathways with an associated interactive software tool. Users can view and download individual pathway maps and browse the entire database from this…

TeloPIN
Data

TeloPIN Telomeric Proteins Interaction Network

A database that points to provide comprehensive information on protein-protein,…

A database that points to provide comprehensive information on protein-protein, protein-DNA and protein-RNA interaction of telomeres. TeloPIN database contains four types of interaction data,…

ADAN
Data

ADAN

A collection of different modular protein domains (SH2, SH3, PDZ, WW, etc.).…

A collection of different modular protein domains (SH2, SH3, PDZ, WW, etc.). ADAN contains 3505 entries with extensive structural and functional information available, manually integrated, curated…

LMPID
Data

LMPID Linear Motif mediated Protein Interaction Database

A manually curated database which provides comprehensive experimentally…

A manually curated database which provides comprehensive experimentally validated information about the linear motifs (LMs) mediating PPIs from all organisms on a single platform. About 2200 entries…

IIIDB
Data

IIIDB

Nowadays, many protein-protein interaction (PPI) databases are available, but…

Nowadays, many protein-protein interaction (PPI) databases are available, but the isoform level PPI prediction database has not been seen yet. IIIDB is a database for isoform-isoform interactions and…

AIM
Data

AIM Arabidopsis Interactome Modules

The database contains almost 250 000 modules that were generated using multiple…

The database contains almost 250 000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using…

PubAngioGen
Data

PubAngioGen

Displays a comprehensive network for exploring the connection between…

Displays a comprehensive network for exploring the connection between angiogenesis and diseases at multilevels including protein-protein interaction, drug-target, disease-gene and signaling pathways…

ComPPI
Data

ComPPI Compartmentalized Protein-Protein Interaction Database

A cellular compartment-specific database of proteins and their interactions…

A cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis. ComPPI enables the user to filter…

VirusMentha
Data

VirusMentha

A virus-virus and virus-host interaction resource build on the detailed…

A virus-virus and virus-host interaction resource build on the detailed curation protocols of the IMEx consortium and on the integration strategies developed for mentha. VirusMentha is regularly and…

Yeast 5
Data

Yeast 5

Expands and refines the computational reconstruction of yeast metabolism and…

Expands and refines the computational reconstruction of yeast metabolism and improves the predictive accuracy of a stoichiometrically constrained yeast metabolic model. It differs from previous…

Wiki-pi
Data

Wiki-pi

A web-based interface to a database of human PPIs, which allows users to…

A web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological…

WormPD
Data

WormPD Worm Proteome Database

Contains comprehensive information on the entire proteome of Caenorhabditis…

Contains comprehensive information on the entire proteome of Caenorhabditis elegans. WormPD comprises individual Locus Reports that are inter-linked to facilitate searching across the multiple…

RKD
Data

RKD Rice Kinase Database

A phylogenomic database to facilitate functional analysis of this large gene…

A phylogenomic database to facilitate functional analysis of this large gene family. Sequence and genomic data, including gene expression data and protein-protein interaction maps, can be displayed…

S/MARt DB
Data

S/MARt DB

Collects information about scaffold/matrix attached regions and the nuclear…

Collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the…

SGMP
Data

SGMP Signaling Gateway Molecule Pages

Provides highly structured data on proteins which exist in different functional…

Provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. A molecule page starts with astate of a native protein, without…

SCOPPI
Data

SCOPPI Structural Classification of Protein-Protein Interface

A database of all domain-domain interactions and their interfaces derived from…

A database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain…

Prolinks
Data

Prolinks

A collection of inferences of functional linkages between proteins using 4…

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…

ProtCid
Data

ProtCid Protein Common interfaces database

A database that contains clusters of similar homodimeric and heterodimeric…

A database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). Such interfaces, especially of homologous but non-identical proteins,…

RAPID
Data

RAPID Resource of Asian Primary Immunodeficiency Diseases

A web-based compendium of molecular alterations in primary immunodeficiency…

A web-based compendium of molecular alterations in primary immunodeficiency diseases. RAPID hosts information on sequence variations and expression at the mRNA and protein levels of all genes…

PiSITE
Data

PiSITE

A database that provides protein-protein interaction sites at the residue level…

A database that provides protein-protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the…

PombePD
Data

PombePD

A component of the Fungal Collection and contains comprehensive information on…

A component of the Fungal Collection and contains comprehensive information on the entire proteome of S. pombe. PombePD comprises individual Locus Reports that are inter-linked to facilitate…

PRIN
Data

PRIN Predicted Rice Interactome Network

Presents a computational approach to predict the protein-protein interactions…

Presents a computational approach to predict the protein-protein interactions in Oryza sativa. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where…

PrePPI
Data

PrePPI

A database of predicted and experimentally determined protein-protein…

A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. Predicted interactions are assigned a likelihood using a Bayesian framework that…

PROFESS
Data

PROFESS PROtein Function, Evolution, Structure and Sequence

A biology database system that integrates databases describing protein…

A biology database system that integrates databases describing protein functions, evolution, structures and sequences. The utility of PROFESS is demonstrated by the analysis of the structural drift…

PPIRA
Data
PIBASE
Data

PIBASE

A collection of all protein structural interfaces extracted from the Protein…

A collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are…

PICCOLO
Data

PICCOLO

A comprehensive relational database capturing the details of structurally…

A comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues…

Pigment Cell…
Data

Pigment Cell Gene Resource

A specialized web-accessible database which contains information on the genetic…

A specialized web-accessible database which contains information on the genetic pathways that regulate pigment cell development and function. This manually curated database is comprised of two…

PIMRider
Data

PIMRider

A web application dedicated to the exploration of protein pathways. Based on…

A web application dedicated to the exploration of protein pathways. Based on reliable Protein Interaction Maps (PIM), PIMRider leads to the unraveling of biological functions.

PIPs
Data

PIPs

A database of predicted human protein-protein interactions. The interactions in…

A database of predicted human protein-protein interactions. The interactions in PIPs were calculated by a Bayesian method that combines information from expression, orthology, domain co-occurrence,…

PINA
Data

PINA Protein Interaction Network Analysis

A comprehensive web resource, which includes a database of unified…

A comprehensive web resource, which includes a database of unified protein-protein interaction data integrated from six manually curated public databases, and a set of built-in tools for network…

PDZBase
Data

PDZBase

A manually curated protein-protein interaction database developed specifically…

A manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein-protein…

PAIR
Data

PAIR Predicted Arabidopsis Interactome Resource

Comprehensive data set of the Arabidopsis interactome with high reliability.…

Comprehensive data set of the Arabidopsis interactome with high reliability. PAIR features a user-friendly query interface, providing rich annotation on the relationships between two proteins. A…

MycoPathPD
Data

MycoPathPD

A component of the Fungal Collection and contains comprehensive information on…

A component of the Fungal Collection and contains comprehensive information on the entire proteomes of Candida albicans and seventeen other human fungal pathogens. MycoPathPD comprises individual…

Negatome
Data

Negatome

A collection of protein and domain pairs which are unlikely engaged in direct…

A collection of protein and domain pairs which are unlikely engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived…

NetPro
Data

NetPro

A comprehensive database of protein-protein and protein-small molecules…

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…

NCPI
Data

NCPI Neurospora Crassa Protein Interactome database

Represents a platform to provide predicted protein-protein interactions (PPIs)…

Represents a platform to provide predicted protein-protein interactions (PPIs) in model fungus Neurospora crassa. This database includes 27,588 predicted PPIs and fourteen only experimental PPIs.…

NURSA
Data

NURSA Nuclear Receptor Signaling Atlas

The mission is to accrue, develop, and communicate information that advances…

The mission is to accrue, develop, and communicate information that advances our understanding of the roles of nuclear receptors (NRs) in human diseases and conditions in which NRs play an integral…

MPI-LIT
Data

MPI-LIT Microbial Protein Interaction database

A dataset focusing on microbial binary protein-protein interactions and…

A dataset focusing on microbial binary protein-protein interactions and associated experimental evidence that we have manually curated from 813 abstracts and full texts that were selected from an…

MPIDB
Data

MPIDB Microbial Protein Interaction DataBase

Aims to collect and provide all known physical microbial interactions.…

Aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and…

MnM
Data

MnM Minimotif Miner

An online database for identifying new minimotifs in protein queries.…

An online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. This online database can be…

MitoInteractome
Data

MitoInteractome Mitochondrial Protein Interactome Database

A web based portal containing information relevant to Mitochondrial Proteins.…

A web based portal containing information relevant to Mitochondrial Proteins. It also serves as a research tool for finding interacting partners and studying mitochondrial diseases. It has a…

MatrixDB
Data

MatrixDB

A freely available database focused on interactions established by…

A freely available database focused on interactions established by extracellular proteins and polysaccharides. MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium…

MiST
Data

MiST Microbial Signal Transduction database

Contains the signal transduction proteins for bacterial and archaeal genomes.…

Contains the signal transduction proteins for bacterial and archaeal genomes. These are identified using various domain profiles that directly or indirectly implicate a particular protein in…

MIPS Mammalian…
Data

MIPS Mammalian Protein-Protein Interaction Database

A resource of high-quality experimental protein interaction data in mammals.…

A resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators.

MINT
Data

MINT Molecular INTeraction Database

A public repository for protein-protein interactions (PPI) reported in…

A public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The web interface allows the users to search, visualize and download interactions data. MINT is one of…

InterMitoBase
Data

InterMitoBase

An integrated platform providing high quality protein-protein interaction (PPI)…

An integrated platform providing high quality protein-protein interaction (PPI) data in human mitochondrion and useful tools to analysis PPI network. Currently there are 490 proteins locating in…

iRefIndex
Data

iRefIndex

A method to generate a key for a protein interaction record and a key for each…

A method to generate a key for a protein interaction record and a key for each participant protein. iRefIndex provides an index of protein interactions available in a number of primary interaction…

IRView
Data

IRView

Contains data for 3417 interacting regions (IRs) in human and mouse proteins.…

Contains data for 3417 interacting regions (IRs) in human and mouse proteins. The data were obtained from different sources and combined with annotated region data from InterPro. Information on…

JAIL
Data

JAIL

The increasing number of solved macromolecules provides a solid number of 3D…

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of…

iMOTdb
Data

iMOTdb

Realization of conserved residues that represent a protein family is crucial…

Realization of conserved residues that represent a protein family is crucial for clearer understanding of biological function as well as for the better recognition of additional members in sequence…

Instruct
Data

Instruct

A database of high-quality, 3D, structurally resolved protein interactome…

A database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction…

ICBS
Data

ICBS Inter-Chain Beta-Sheets

A comprehensive database of interchain beta-sheet (ICBS) interactions that is…

A comprehensive database of interchain beta-sheet (ICBS) interactions that is updated on a weekly basis and allows entries to be sorted and searched by relevance and other criteria through a simple…

InterEvol…
Data

InterEvol database

It was designed for exploring 3D structures of homologous interfaces of protein…

It was designed for exploring 3D structures of homologous interfaces of protein complexes. For every chain forming a complex in the protein data bank (PDB), close and remote structural interologs…

I2D
Data

I2D Interologous Interaction Database

An on-line database of known and predicted mammalian and eukaryotic…

An on-line database of known and predicted mammalian and eukaryotic protein-protein interactions. I2D has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally…

hp-DPI
Data

hp-DPI helicobacter pylori Database of Protein Interactomes

A database of experimental and predicted protein-protein interactions in…

A database of experimental and predicted protein-protein interactions in Helicobacter pylori. hp-DPI is developed with a succinct yet comprehensive visualization tool integrated with annotation from…

HPIDB
Data

HPIDB

Facilitates both the identification and functional analysis of host–pathogen…

Facilitates both the identification and functional analysis of host–pathogen interactions (HPI) for a broad range of pathogens and their hosts. HPIDB 2.0 provides targeted curation, integration…

Human…
Data

Human Proteinpedia

A community portal for sharing and integration of human protein data. It allows…

A community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD)…

HuPI
Data

HuPI Human Proteotheque Initiative

A multidisciplinary project aimed at building a repertoire of comprehensive…

A multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks. The information contained in the Proteotheque is made publicly available…

HCVpro
Data

HCVpro Hepatitis C Virus protein interaction database

A comprehensive and integrated HCV-specific knowledgebase housing consolidated…

A comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet,…

HINT
Data

HINT High-quality INTeractomes

A database of high-quality protein-protein interactions in different organisms.…

A database of high-quality protein-protein interactions in different organisms. These have been compiled from different sources and then filtered both systematically and manually to remove erroneous…

HitPredict
Data

HitPredict

A consolidated resource of experimentally identified, physical protein-protein…

A consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. HitPredict provides a manually curated dataset of 398…

HAPPI
Data

HAPPI Human Annotated and Predicted Protein Interaction

A free, open-access, and comprehensive database collection of computer…

A free, open-access, and comprehensive database collection of computer annotated human protein-protein interactions from public data sources and computational predictions. The HAPPI database was…

HCPIN
Data

HCPIN Human Cancer Pathway Protein Interaction Network

Provides a comprehensive description of this biomedically important…

Provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research. To…

HIV-1, Human Protein Interaction Database
Data
FunCoup
Data

FunCoup

A database that maintains and visualizes global gene/protein networks of…

A database that maintains and visualizes global gene/protein networks of functional coupling that have been constructed by Bayesian integration of diverse high-throughput data. FunCoup distinguishes…

GWIDD
Data

GWIDD Genome-Wide Docking Database

Offers an extensive source of data for structural studies of protein-protein…

Offers an extensive source of data for structural studies of protein-protein complexes on genome scale. The current release of the database combines the available experimental data on the structure…

DIPOS
Data

DIPOS Database of Interacting Proteins in Oryza Sativa

Provides comprehensive information of interacting proteins in rice, where the…

Provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain based methods. DIPOS contains 14…

DOMMINO
Data

DOMMINO

A comprehensive database of macromolecular interactions that includes the…

A comprehensive database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. The database…

ComSin
Data

ComSin

Most of the proteins in a cell assemble into complexes to carry out their…

Most of the proteins in a cell assemble into complexes to carry out their function. ComSin is a database of protein structures in bound (complex) and unbound (single) states to provide a researcher…

CutDB
Data

CutDB

Focuses on the annotation of individual proteolytic events, both actual and…

Focuses on the annotation of individual proteolytic events, both actual and predicted. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and…

DAnCER
Data

DAnCER Disease Annotated Chromatin Epigenetics Resource

Integrates information on genes with chromatin modification function from five…

Integrates information on genes with chromatin modification function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture,…

AtPIN
Data

AtPIN Arabidopsis thaliana Protein Interaction Network

A database and web interface for searching and building interaction networks…

A database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. AtPIN is a friendly and easy-to-use tool that aggregates…

BIND
Data

BIND Biomolecular Interaction Network Database

Archives biomolecular interaction, complex and pathway information. A web-based…

Archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND includes a BIND Query and Submission interface, a Standard…

CCSB…
Data

CCSB Interactome Database

A database of binary protein-protein interactions for a number of different…

A database of binary protein-protein interactions for a number of different organisms. The long-term goal of CCSB is to understand how macromolecular networks control biological processes and how…

KEGG BRITE
Data

KEGG BRITE

A collection of manually created hierarchical text (htext) files capturing…

A collection of manually created hierarchical text (htext) files capturing functional hierarchies of various biological objects, especially those represented as KEGG objects. In contrast to KEGG…

3did
Data

3did

A catalog of protein-protein interactions for which a high-resolution 3D…

A catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data…

AS-ALPS
Data

AS-ALPS Alternative Splicing-induced ALteration of Protein Structure

A database which provides information that would be useful for analyzing the…

A database which provides information that would be useful for analyzing the effects of alternative splicing (AS) on protein structure, interactions with other bio-molecules and protein interaction…

IntAct
Data

IntAct

Provides a freely available, open source database system and analysis tools for…

Provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are…

SynSysNet
Data

SynSysNet Synaptic Proteins Database

Provides a platform that creates a comprehensive 4D network of synaptic…

Provides a platform that creates a comprehensive 4D network of synaptic interactions. Protein-protein interactions and drug-target interactions can be viewed as networks; corresponding PubMed IDs or…

TRIP Database
Data

TRIP Database TRansient receptor potential channel-Interacting Protein Database

A manually curated database that aims to offer comprehensive information on…

A manually curated database that aims to offer comprehensive information on protein-protein interactions (PPIs) of mammalian Transient receptor potential (TRP) channels. The TRIP Database has…

DIP
Data

DIP Database of Interacting Proteins

Catalogs experimentally determined interactions between proteins. DIP combines…

Catalogs experimentally determined interactions between proteins. DIP combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data…

DOMINE
Data

DOMINE

A database of known and predicted protein domain (domain-domain) interactions.…

A database of known and predicted protein domain (domain-domain) interactions. It contains interactions inferred from PDB entries, and those that are predicted by 13 different computational…

DroID
Data

DroID Drosophila Interactions Database

A comprehensive gene and protein interactions (interactome) database designed…

A comprehensive gene and protein interactions (interactome) database designed specifically for the model organism Drosophila. The database includes protein-protein, TF-gene, miRNA-gene, and genetic…

VirHostNet
Data

VirHostNet Virus-Host Network

A public knowledge base specialized in the management and analysis of…

A public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. VirHostNet will…

3D-Interologs
Data

3D-Interologs

A cross-species interacting database inferring from three-dimensional (3D)…

A cross-species interacting database inferring from three-dimensional (3D) protein structure complexes and a novel scoring function by using 3D-domain interologs. For a query protein, the…

BISC
Data

BISC BInary SubComplex Database

A protein-protein interaction (PPI) database linking up the two communities…

A protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers…

CPDB
Data

CPDB ConsensusPathDB

A meta-database that integrates different types of functional interactions from…

A meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. The ConsensusPathDB web interface allows users to take advantage of these…

IMEx
Data

IMEx International Molecular Exchange

An international collaboration between major public interaction data providers…

An international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search…

ARNIE
Data

ARNIE AVEXIS Receptor Network with Integrated Expression

An online database that integrates the extracellular protein interaction…

An online database that integrates the extracellular protein interaction network. ARNIE allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal…

HTRIdb
Data

HTRIdb

An open-access database that can be searched via a user-friendly web interface…

An open-access database that can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or…

T2D@ZJU
Data

T2D@ZJU Type 2 diabetes mellitus @ZJU

A comprehensive and up-to-date knowledgebase for type 2 diabetes mellitus…

A comprehensive and up-to-date knowledgebase for type 2 diabetes mellitus (T2D). T2D@ZJU contains three levels of heterogeneous connections associated with T2D, which is retrieved from pathway…

PathPPI
Data

PathPPI

An integrated dataset of human pathways and protein-protein interactions. We…

An integrated dataset of human pathways and protein-protein interactions. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein…

SPiD
Data

SPiD

An online database for exploring networks of interacting proteins in Bacillus…

An online database for exploring networks of interacting proteins in Bacillus subtilis characterized by the two-hybrid system. Graphical displays of interaction networks are created dynamically as…