Tag: protein-protein interactions

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

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.

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 ...

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT ...

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

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.

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 ...

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 ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

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 ...

Structure Function Linkage Database (SFLD) is a database of enzymes classified by linking sequences to chemical function. A hierachical systems is used to classify enzymes by family or superfamily other category levels include functional domain, subg ...

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 ...

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.

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

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans ( ...

The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools for the biology and genetics of ageing. HAGR features several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing i ...

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, ...

Protein interaction predictions by several different methods

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

Known and predicted protein domain interactions observed in PDB entries,

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. ...

CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, pro ...

Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.

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

Data Repository for Yeast Genetic Interaction Networks

A database of non-interacting proteins

Protein Common Interface Database

Quality assessed protein-protein interactions in 9 species

A non-redundant database of protein-peptide complexes

Predicted Arabidopsis Interactome Resource

Domain interaction map: experimental and predicted protein domain interactions

IsoRank PPI Network Alignment Based Ortholog Database

Integration, navigation, visualization, and analysis of gene interaction networks. This record has been marked as "Uncertain" because its homepage no longer exists. If you have any information on the current status of this resource, please contact us ...

Arabidopsis thaliana Protein Interactome Database

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

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an an ...

Protein-protein interactions for mammalian TRP channels

Database for integration of human functional interactions

Interacting and non-interacting protein pairs

Presaging Critical Residues in Protein interface DataBase

Binary SubComplexes in Proteins Database

The signal molecules and pathways are classified and illustrated by graphs in this database.

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.

Domain peptide interactions

Predicted human protein-protein interactions

Protein-protein interactions involving PDZ domains

Predicted and experimentally determined protein-protein interactions for yeast and human

Interacting residues in protein-protein interfaces in PDB

Host-pathogen protein-protein interactions

Protein-protein interactions in various evolutionary lineages

Protein-protein interfaces in co-crystallized protein structures

Putative protein domain interactions

Protein-protein interactions mediated by interchain beta-sheet formation

Joint Evolutionary Trees: Protein-protein interaction patches in known structures

Database of protein interactions in Helicobacter pylori

The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains more than 1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information. Each ...

Human protein interactions mediated by phosphoprotein-binding domains

Human protein interaction database

A database on the structural synaptome

Hot spots (functionally and structurally important residues) in protein interfaces

Network approach to human protein kinases and their substrate proteins

Binding Mother of All Databases: a database of protein-ligand crystal structures

The Protein Kinase Resource (PKR) is a curated information source which provides an integrated view of sequence and structure data combined with biochemical and genetic function data focused on a single family of proteins, the protein kinases. In add ...

Pathguide: the Pathway Resource List (http://pathguide.org) is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic pathways, signaling pathways, tran ...

Macromolecular complexes from key model organisms

Online maps of metabolic and signaling pathways

Systematic mapping of protein-protein interactions (PPIs) has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated interaction datasets are valuable resources for sci ...

Genes and proteins involved in human and yeast cell cycle

SCOPPI is 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 associations and are annotated with various in ...

High-throughput experiments are being performed at an ever-increasing rate to systematically elucidate protein-protein interaction (PPI) networks for model organisms, while similar experiments for human networks have lagged far behind. The Online Pre ...

The Noncoding RNAs and Protein related biomacromolecules Interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between nonc ...

Het-PDB Navi is a database that collects small molecules found in Protein Data Bank (PDB). An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from t ...

The Affinity Database 'AffinDB' contains affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure. As of Monday, November 28th, 2005, AffinDB con ...

Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Wnt genes and Wnt signaling are also implicated in cancer. Insights into the mechanisms of Wnt action have emerg ...

Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the s ...

SENTRA (http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html) is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and meth ...

Structural motifs are central to the integrity of the fold and require careful analysis for their identification. IMOTdb is a repertoire of spatially interacting motifs in single protein structures as well as those among distantly related protein str ...

PathoPlant® has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. Signal transduction pathways are modeled as consecutive sequences of known m ...

Better characterization of binding sites in proteins and the ability to accurately predict their location and energetic properties are major challenges which, if addressed, would have many valuable practical applications. Unfortunately, reliable benc ...

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways, and kinetic characteristics of elementary processes. In the past two years, the GeneNet structure was considerably im ...

CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. CellCircuits captures ...

TRANSPATH® is a database on signal transduction pathways that are modeled as bipartite graphs with molecules and reactions as node classes [1,2,3,4,5]. The molecule entries include polypeptides, modified forms, multicomponent complexes, high-order ab ...

G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GLIDA is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information ...

EndoNet is a new database that provides information about the components of endocrine networks and their relations. It focuses on the endocrine cell-to-cell communication and enables the analysis of intercellular regulatory pathways in humans. In the ...

In past number of databases (e.g. MHCPEP, MHCBN, AntijenDB, IEDB, BCIPEP, IMGT) have been developed to assists the researchers working in the field of adaptive immunity. Best of author’s knowledge no method have been developed in the field of ...

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals ...