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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…
BioPlex
Dataset

BioPlex

Reflects cellular localization, biological process, and molecular function,…

Reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. BioPlex structure also reveals associations among thousands…

NeuroDNet
Dataset

NeuroDNet

Contains comprehensive information about the twelve neurodegenerative diseases…

Contains comprehensive information about the twelve neurodegenerative diseases under one portal. NeuroDNet offers to user a bouquet of tools and features to analyze the information by creating…

dbEMT
Dataset

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…

BioGRID
Dataset

BioGRID Biological General Repository for Interaction Datasets

Houses genetic and protein interactions curated from the primary biomedical…

Houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. BioGRID contains 749 912 interactions as drawn from 43 149…

AtPID
Dataset

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…

Human…
Dataset

Human protein-protein interaction network

Provides information about more than 3000 protein-protein interactions (PPIs).…

Provides information about more than 3000 protein-protein interactions (PPIs). Human PPI network assists users to better understand the functional organization of proteome. During the research, users…

HuRI
Dataset

HuRI Human Reference Protein Interactome Mapping Project

Generates map about protein-protein interactome network. HuRI is a database…

Generates map about protein-protein interactome network. HuRI is a database that can identify binary protein-protein interactions (PPIs) by interrogating all pairwise combinations of predicted human…

MINT
Dataset

MINT Molecular INTeraction Database

Stores, in a structured format, information about molecular interactions by…

Stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. The new version of MINT is based on a…

IMEx
Dataset

IMEx International Molecular Exchange

Stores a non-redundant set of protein interactions. IMEx is a consortium that…

Stores a non-redundant set of protein interactions. IMEx is a consortium that made a data resource, which enables user to download, combine, visualize and analyze data in a single format from…

CCSB…
Dataset

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…

S/MARtDB
Dataset

S/MARtDB scaffold/matrix attached regions transaction database

Covers scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins…

Covers scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are implicated in the chromosomal attachment to the nuclear scaffold. S/MARtDB was constructed by collecting data in…

HitPredict
Dataset

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…

InWeb_IM
Dataset

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,…

Hu.MAP
Dataset

Hu.MAP human protein complex MAP

Provides a comprehensive global map of human protein complexes. Hu.MAP consists…

Provides a comprehensive global map of human protein complexes. Hu.MAP consists of predominately core human complexes and covers a large fraction of disease genes. The database contains complexes,…

TissueNet
Dataset

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
Dataset

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.…

APID…
Dataset

APID Interactomes

Identifies and handles all the proteins and maps them into the reference…

Identifies and handles all the proteins and maps them into the reference proteomes of each species. APID is a bioinformatics database developed to provide protein interactomes at different quality…

DIP
Dataset

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…

IntAct
Dataset

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…

PCoM-DB
Dataset

PCoM-DB

Stores the analyzed data with a user-friendly interface. PCoM-DB is an online…

Stores the analyzed data with a user-friendly interface. PCoM-DB is an online database that can help users to find novel protein complexes in Arabidopsis thylakoids and Synechocystis. It provides…

Prolinks
Dataset

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…

I2D
Dataset

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…

PIMRider
Dataset

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.

VirHostNet
Dataset

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…

HIV-1, Human Protein Interaction Database
Dataset
CPDB
Dataset

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…

FunCoup
Dataset

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…

PINA
Dataset

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…

WormPD
Dataset

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…

3did
Dataset

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…

PIPs
Dataset

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,…

MatrixDB
Dataset

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…

SCOPPI
Dataset

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…

HAPPI
Dataset

HAPPI Human Annotated and Predicted Protein Interaction

Gathers a set of computer-annotated human protein-protein interactions (PPIs)…

Gathers a set of computer-annotated human protein-protein interactions (PPIs) from public data sources and computational predictions. HAPPI supports a wide range of biomedical research applications,…

Negatome
Dataset

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…

DOMINE
Dataset

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…

PrePPI
Dataset

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…

MIPS Mammalian…
Dataset

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.

CutDB
Dataset

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…

EchoBASE
Dataset

EchoBASE

Contains some information from post-genomic experiments that use the model…

Contains some information from post-genomic experiments that use the model bacterium Escherichia coli K12. EchoBASE allows consultation of protein–protein interaction (PPI) data, structural data and…

ProtCid
Dataset

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,…

PepX
Dataset

PepX Protein-peptide complexes

Provides information about protein-peptide complexes available in the Protein…

Provides information about protein-peptide complexes available in the Protein Data Bank (PDB). PepX concerns protein-peptide complexes with peptide lengths up to 35 residues. It provides an…

RKD
Dataset

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…

HPIDB
Dataset

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 with…

PDZBase
Dataset

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…

SNAPPI-DB
Dataset
PIBASE
Dataset

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…

MnM
Dataset

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…

ComSin
Dataset

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…

S/MARt DB
Dataset

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…

InterEvol…
Dataset

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…

PiSITE
Dataset

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…

RAPID
Dataset

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…

MPIDB
Dataset

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…

HCPIN
Dataset

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…

iRefIndex
Dataset

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…

IID
Dataset

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…

InsectBase
Dataset

InsectBase

Provides a comprehensive platform for researchers who have interests in…

Provides a comprehensive platform for researchers who have interests in analyzing insect genes. InsectBase contains more than 12 millions of sequences, encompassing the genomes of 138 insects,…

SIGNOR
Dataset

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…

DBETH
Dataset

DBETH Database for Bacterial ExoToxins

The main objective of this database is to provide a comprehensive knowledgebase…

The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based…

PROXiMATE
Dataset

PROXiMATE

Provides unbiased training and validation datasets for the development of…

Provides unbiased training and validation datasets for the development of algorithms to predict binding affinity changes due to missense mutations. The PROXiMATE database helps about the study of…

PCPPI
Dataset

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).…

AS-ALPS
Dataset

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…

SynSysNet
Dataset

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…

RicePPINet
Dataset

RicePPINet

Provides an expanded landscape of computational interactome for genetic…

Provides an expanded landscape of computational interactome for genetic dissection of agronomically important traits in rice. RicePPINet is a genome-wide rice protein-protein interaction (PPI)…

DD
Dataset

DD Database of Death Domain

Provides comprehensive information on protein–protein interactions (PPIs) of…

Provides comprehensive information on protein–protein interactions (PPIs) of the Death Domain (DD) superfamily. The DD database is manually curated and offers a user-friendly interface with many…

HTRIdb
Dataset

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…

Instruct
Dataset

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…

DroID
Dataset

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…

ARNIE
Dataset

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…

DIIP
Dataset

DIIP Domain-based Isoform Interactome Prediction

Allows users to predict the isoform interactome from an experimentally…

Allows users to predict the isoform interactome from an experimentally determined reference interactome. DIIP permits users to find several informations about human protein-protein interactions…

DOMMINO
Dataset

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…

DAnCER
Dataset

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,…

PINdb
Dataset

PINdb Proteins Interacting in the Nucleus database

Provides a specialized knowledge base for proteomics research. PINdb is an…

Provides a specialized knowledge base for proteomics research. PINdb is an online resource focuses on multiprotein nuclear complexes from human or yeast cells that have been biochemically and/or…

HINT
Dataset

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…

KUPS
Dataset

KUPS University of Kansas Proteomics Service

Provides high-quality protein-protein interaction (PPI) datasets for…

Provides high-quality protein-protein interaction (PPI) datasets for researchers who are interested in elucidating PPIs with 'in silico' methods. Additionally, KUPS provides two benchmark…

PPIM
Dataset

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…

AraPPINet
Dataset

AraPPINet Arabidopsis Protein-Protein Interaction Network

A genome-wide protein interaction network that is inferred from both…

A genome-wide protein interaction network that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574…

ICBS
Dataset

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…

PubAngioGen
Dataset

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
Dataset

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…

Complex Portal
Dataset

Complex Portal

A manually curated, encyclopaedic resource of macromolecular complexes from a…

A manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. All data is freely available for search and download. The Complex Portal is hosted by the…

PepBase
Dataset

PepBase

Gathers information about mass spectrometry (MS)/MS spectra. PepBase is a…

Gathers information about mass spectrometry (MS)/MS spectra. PepBase is a peptide database that consists in a grouping of experimental data handled by a single analytical platform at the proteomics…

JAIL
Dataset

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…

Yeast 5
Dataset

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…

PPI4DOCK
Dataset

PPI4DOCK

A large benchmark set for studying protein docking/scoring methods. PPI4DOCK…

A large benchmark set for studying protein docking/scoring methods. PPI4DOCK contains 1417 non-redundant docking targets between two subunits. Each subunit is a protein model obtained by homology…

AtPIN
Dataset

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…

RiceGeneThreshe…
Dataset

RiceGeneThresher

A public online resource for mining genes underlying genome regions of interest…

A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome.

BISC
Dataset

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…

FPPI
Dataset

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…

DOCKGROUND
Dataset

DOCKGROUND

Helps user to better understand and develop structural modelling of protein…

Helps user to better understand and develop structural modelling of protein complexes. Dockground is resource for structural modeling of protein interactions. It offers a variety of interconnected…

PRIN
Dataset

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…

MauPIR
Dataset

MauPIR Macrotyloma uniflorum Protein Interaction Resource

Predictes protein-protein interactions (PPis) in Horsegram (Kulthi). MauPIR…

Predictes protein-protein interactions (PPis) in Horsegram (Kulthi). MauPIR provides high confidence systems biology information for horsegram genes, proteins and involved processes. Highly reliable…

MPI-LIT
Dataset

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…

AraPPISite
Dataset

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…

MitoInteractome
Dataset

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…

SGMP
Dataset

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…

Wiki-pi
Dataset

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…

PICCOLO
Dataset

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…

3D-Interologs
Dataset

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…

CMGSDB
Dataset

CMGSDB Database for Computational Modeling of Gene Silencing

An integration of heterogeneous data sources about Caenorhabditis elegans with…

An integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains.

iMOTdb
Dataset

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…

BIND
Dataset

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…

Piface
Dataset

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…

TarNet
Dataset

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…

A A A
MiasDB
Dataset

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…

PICKLE
Dataset

PICKLE Protein InteraCtion KnowLedgebasE

Provides a bottom-up solution to the node set standardization problem. PICKLE…

Provides a bottom-up solution to the node set standardization problem. PICKLE is a meta-database for direct human protein-protein interactions (PPIs) network. This genetic information ontology…

OncoPPi Portal
Web

OncoPPi Portal

Allows access, manipulation, and interpretation of a high-quality…

Allows access, manipulation, and interpretation of a high-quality cancer-focused network of protein-protein interactions (PPIs). OncoPPi Portal is a web application combining several functions: (1)…

SCENERY
Web

SCENERY Single CEll NEtwork Reconstruction sYstem

Allows analysis of cytometry data. SCENERY is a web application permitting…

Allows analysis of cytometry data. SCENERY is a web application permitting users to upload their data and configure the study of their data. It provides a wide range of data analysis methods…

SalmoNet
Dataset

SalmoNet

Gathers network data (metabolic, regulatory, protein-protein interaction) for…

Gathers network data (metabolic, regulatory, protein-protein interaction) for 10 representative pathogenic Salmonella strains. SalmoNet is an online database regrouping information on interactions…

GMO
Dataset

GMO Gametogenesis Molecule Online

Allows analysis of the gametogenesis dynamics and modularity in both human and…

Allows analysis of the gametogenesis dynamics and modularity in both human and mouse species. GMO is an online repository providing information about gametogenesis modules and genes. It informs about…

GAPI
Web

GAPI Geometric Analysis of the Protein Interactome

Provides a web tool for the geometric analysis of the human protein interaction…

Provides a web tool for the geometric analysis of the human protein interaction network (hPIN). GAPI can compute hyperbolic distances between proteins, which hint at their likelihood of interaction.…

DifferentialNet
Dataset

DifferentialNet

Serves for differential network analysis of human tissue interactomes.…

Serves for differential network analysis of human tissue interactomes. DifferentialNet is an online resource containing current data of experimentally-detected PPIs with data of gene expression…

Tabloid…
Dataset

Tabloid Proteome

Provides unique added value for researchers that are interested in…

Provides unique added value for researchers that are interested in understanding the relations between proteins. Tabloid Proteome is an easily searchable website that presents protein associations…

TrypsNetDB
Dataset

TrypsNetDB

Provides information to allow a better characterization of the queried proteins…

Provides information to allow a better characterization of the queried proteins in the species of interest. TrypsNetDB is a database that automatically performs inter-species mapping of the available…

KEGG BRITE
Dataset

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…

mpMoRFsDB
Dataset

mpMoRFsDB Database of Molecular Recognition Features in Membrane Proteins

Supplies information concerning disorder-based protein–protein interactions…

Supplies information concerning disorder-based protein–protein interactions (PPIs) in membrane proteins. mpMoRFsDB is a database that collects and provides information about molecular recognition…

PCDq
Dataset

PCDq

Predicts human protein complexes from integrated Protein-Protein Interaction…

Predicts human protein complexes from integrated Protein-Protein Interaction (PPI) network data. PCDq is a human protein complex database with quality index, which tells evidence level as members of…

MppDB
Dataset

MppDB Mouse protein-protein interaction DataBase

A mouse protein-protein interaction (PPI) database. The mouse protein…

A mouse protein-protein interaction (PPI) database. The mouse protein interaction dataset is stored in the Mouse protein-protein interaction DataBase (MppDB) that is useful source of information for…

hp-DPI
Dataset

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…

PombePD
Dataset

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…

MycoPathPD
Dataset

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…

DIPOS
Dataset

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…

TRIP Database
Dataset