Tag: protein interaction


Found 136 sources
Source Match ReputationScore*

Kyoto Encyclopedia of Genes and Genomes


KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by geno ...
100%

STRING


STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.
96%

Reactome - a curated knowledgebase of biological pathways


REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.
95%

Biological General Repository for Interaction Datasets


The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.
93%

IntAct molecular interaction database


IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all ...
93%

Comparative Toxicogenomics Database


Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...
85%

Molecular INTeraction database


MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. As of September 2013, This resource uses the IntAct database framework to help reduce the effort of scientists and improve o ...
83%

Database of Interacting Proteins


The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions
80%

FlyBase


Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...
77%

WormBase


WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...
71%

Human Protein Reference Database


The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...
70%

InnateDB


InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...
63%

Eukaryotic Linear Motifs


This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs ...
58%

Interologous Interaction Database


I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs).
57%

FlyMine


FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
57%

BindingDB database of measured binding affinities


BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
57%

CORUM


CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, su ...
57%

VirHostNet 2.0


VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.
55%

MatrixDB: Extracellular Matrix Interaction Database


MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...
55%

Universal PBM Resource for Oligonucleotide Binding Evaluation


The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.
55%

SIGnaling Network Open Resource


The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...
55%

H-Invitational Database


H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...
54%

VirusMentha


VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...
54%

Animal Transcription Factor Database


AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...
53%

Complex Portal


The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is fr ...
52%

Protein Interaction Network Analysis platform


Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...
52%

3D interacting domains


The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...
52%

The Chemical Probes Portal


The Chemical Probes Portal is an online open access catalog of annotated small molecule inhibitors, agonists and other chemical tools for biological research and preclinical drug discovery. Annotations for are extensive and distinguish between activi ...
52%

BIND: The Biomolecular Interaction Network Db


Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
51%

HotRegion


Database of interaction Hotspots across the proteome. Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Ho ...
50%

SignaLink


SignaLink is an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. it allows browsing of signaling pathways, cross-talks and multi-pathway proteins; selection of transcriptional, post- ...
50%

GenomeNet


Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W).
50%

Gene3D


Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.
50%

ionomicHUB


ionomicHUB provides curated ionomic data on many thousands of plant samples freely available to the public. It is an international collaborative cyber research environment to help identify and understand the genes and gene networks that function to c ...
49%

Human Protein-Protein Interaction rEference


HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.
49%

TargetMine


TargetMine integrates many types of data for human, rat and mouse. Flexible queries, export of results and data analysis are available.
48%

PDZBase


PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions.
48%

The human DEPhOsphorylation Database


DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...
48%

Network of Cancer Genes


The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...
48%

Host Pathogen Interaction Database


HPIDB 3.0 is a resource that helps annotate, predict and display host-pathogen interactions (HPI). HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB is a host-pathogen protein-protein interaction ( ...
48%

mentha


mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated ...
47%

Agile Protein Interactomes Dataserver


APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome ...
47%

OmniPath


A collection of literature-curated human and rodent signalling pathways. Aggregates over 50 sources in total, ~ 32 for PPIs including SigNOR and BioGRID
47%

PTMcode


PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins.
46%

HIV-1 Human Interaction Database


The HIV-1, human protein interaction data presented here are based on literature reports. This dataset is available in report pages per HIV-1 protein and is also integrated into Entrez Gene report pages for HIV-1 and human proteins.
46%

Pocketome: an encyclopedia of small-molecule binding sites in 4D


The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is invo ...
46%

Interolog Regulog Database


Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.
46%

Protein-Chemical Structural Interactions


Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.
46%

Compendium of Protein Lysine Modifications


CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs).
46%

Minimotif Miner 3.0


A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.
46%

Nematode.net


Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...
45%

Networks of Functional Coupling of proteins


FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of d ...
45%

Protein-ligand affinity change upon mutation


Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.
45%

database of Disease-Gene Associations with annotated Relationships


eDGAR is a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each heterogeneous or polygenic disease, eDGAR provides information on the relationship among the proteins encoded by ...
45%

Protein Protein Interaction Inhibition Database


2P2Idb is a hand-curated structural database dedicated to the modulation of protein-protein interactions (PPIs). It includes all interactions for which both the protein-protein and protein-modulator complexes have been structurally characterized by X ...
45%

Target Central Resource Database


TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiati ...
45%

Interaction Reference Index Web Interface


iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, M ...
45%

DroID - Drosophila Interactions Database


DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...
45%

EciD


Protein interaction predictions by several different methods
45%

Bacterial Protein Interaction Database


Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.
44%

ChannelsDB


ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank.
44%

PathBank


PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...
44%

Pocket Similarity Search using Multiple-Sketches


POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid ex ...
43%

DOMINE


Known and predicted protein domain interactions observed in PDB entries,
43%

PROMISCUOUS


Protein-protein and drug-protein interactions for studies of drug repositioning
43%

PROFEAT


Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for pept ...
43%

IBIS


Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites
42%

Microbial Protein Interaction Database


The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well a ...
42%

PRIDB


Protein-RNA Interface Database
42%

Negatome


A database of non-interacting proteins
42%

HitPredict


Quality assessed protein-protein interactions in 9 species
41%

Mutual Folding Induced by Binding Database


Mutual Folding Induced by Binding (MFIB) is a repository of protein complexes for which the folding of each constituent protein chain is coupled to the interaction forming the complex. This means that while the complexes are stable enough to have the ...
41%

TcoF-DB


Database for Human Transcription Co-Factors
41%

RegPhos


Regulatory Network in Protein Phosphorylation
41%

PAIR


Predicted Arabidopsis Interactome Resource
41%

PespotDB


Web resource designed to provide a central repository for the storage and the analysis of data on domain peptide recognition obtained with interaction assays exploiting peptide chip technology.
41%

Death Domain Database


Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.
41%

TissueNet v.2


Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. ...
41%

Ligand Expo


Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molec ...
41%

Isobase


IsoRank PPI Network Alignment Based Ortholog Database
40%

PSI Molecular Interaction Controlled Vocabulary


A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. The Molecular Interactions Working group page can be found at http://www.psidev.i ...
40%

BINDTranslation


A database of curated biomolecular interactions.
40%

Human Integrated Pathway Database


Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super ...
40%

DIMA


Domain interaction map: experimental and predicted protein domain interactions
39%

AtPID


Arabidopsis thaliana Protein Interactome Database
39%

GWIDD


Genome-WIde Docking Database: 3D structures of protein complexes
39%

Manually Curated Database of Rice Proteins


‘Manually Curated Database of Rice Proteins’ (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 resear ...
38%

Yeast KID


Contains high- and low-throughput data relevant to phosphorylation events. It includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments.
38%

TRIP


Protein-protein interactions for mammalian TRP channels
38%

DOMMINO


Database of MacroMolecular INteractions
38%

Structure, Interfaces and Alignments for Protein-Protein Interactions Database


SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nu ...
38%

PICKLE


A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source informa ...
38%

PPIM


Protein-Protein Interaction database for Maize.
38%

Automatic molecular interaction predictions


InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interac ...
37%

Protein-ligand interaction ontology


The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. PLIO represents knowledge about the interaction o ...
37%

KUPS


Interacting and non-interacting protein pairs
37%

mutLBSgeneDB


Mutations in Ligand Binding Sites gene DataBase
37%

The database of eukaryotic RNA binding proteins


EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...
37%

PCRPi-DB


Presaging Critical Residues in Protein interface DataBase
37%

ePlant


Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.
37%

BISC


Binary SubComplexes in Proteins Database
36%

VHLdb


A database of interactors and mutations of the human von Hippel-Lindau tumor suppressor protein (pVHL).
36%

PDID


Database of molecular-level putative protein-drug interactions in the structural human proteome.
36%

STING


The Blue Star STING database stores information on the interactions between proteins and other bio macromolecules. Structure descriptors used in the analysis of these interactions are stored in STING DB to aid research primarily into the problems cha ...
36%

RNAct


Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise ...
36%

PROtein-protein compleX MutAtion ThErmodynamics Database


PROXiMATE is a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and funct ...
35%

oRNAment


A database of putative RNA binding protein target sites in the transcriptomes of model species. Dashboard - Overview of the database. Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes. Here, we developed a computational tool ...
35%

Tabloid Proteome


an annotated database of protein associations. Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE.These associations represent a broad scala of biological a ...
35%

Vertebrate Secretome Database


Vertebrate Secretome Database (VerSeDa) stores information about proteins that are predicted to be secreted through the classical and non-classical mechanisms, for the wide range of vertebrate species deposited at the NCBI, UCSC and ENSEMBL sites.
35%

ConsensusPathDB


Database for integration of human functional interactions
35%

Translocatome


Translocatome is a database that collects and characterises manually curated and predicted translocating proteins from human cells. The prediction is made by a gradient boosting based machine learning algorithm (XGBoost), using highly curated positiv ...
34%

PlanExp


PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.
34%

Disordered Binding Sites Database


Disordered Binding Sites (DIBS) is a repository of protein complexes that are formed by ordered and disordered proteins. Intrinsically disordered proteins (IDPs) do not have a stable 3D structure in isolation and therefore they defy structure determi ...
34%

OmicsDB.org


OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...
34%

OncoPPi


Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of ne ...
34%

ophid


A Focus on the Integrated Interactions Database (IID). Integrated Interactions Database. tissue specific PPI networks across species.
34%

PsyMuKB


An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translationa ...
33%

Compartmentalized Protein-Protein Interaction


The compartmentalized protein-protein interaction database (ComPPI), provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.
32%

KLIFs


Kinase-ligand Interaction Fingerprints and Structures
32%

AREsite


AU-rich elements in vertebrate mRNA UTR sequences
32%

EvoPPI


EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species.
30%

BioPlex 2.0


A repository of protein interaction data from mass spectrometry experiments.
30%

PDZscape


PDZscape is a compilation of all existing PDZ-containing proteins on a single platform. It provides a user friendly search interface that enables the database to be queried using the names and external identifiers.
30%

Human Reference Protein Interactome Mapping Project


The Human Reference Protein Interactome Mapping Project (HuRI) is a repository, created by the Center for Cancer Systems Biology (CCSB) at Dana-Farber Cancer Institute, which stores the data from the ongoing work on the first complete reference map o ...
30%

iRefIndex


Provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB and MPPI.
30%

PSICQUIC view


Standardises programmatic access to molecular interaction databases.
30%

PDEStrIAn


The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein ...
30%

Protein Contacts Atlas


An interactive resource of non-covalent contacts from over 100,000 publicly available crystal structures in the Protein Data Bank
30%

PSIQUIC (DIP)


Database which catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. Search the database using a protein id.
30%

BIPA


Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces.
30%

SCOWL


PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent.
30%

CrosstalkDB


Repository and statistical tools for directly determined PTM crosstalk based on long peptides measured by mass spectrometry. Focus on histone proteins.
30%

Gliome database


A comprehensive web-based tool to access and analyze glia secretome data. Gliome Database has the following feature regarding glia-secreted proteins.
30%

DistAA


Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interaction ...
30%

JASPAR RESTful API


Widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language ...
30%

S2RSLDB


Sigma-2 receptor selective Ligands Database is an online ligand database consisting of the Sigma-2 selective receptor ligand published since 1993. The S2RSLDB is based on structural 2D information as well as pharmacological and computed physicochemic ...
30%

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