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. These databases are used by researchers interested in examining detailed information on particular proteins.
Assists in the capture of biological interaction data from the primary biomedical literature. BioGRID builds collection and creates annotations of genetic and protein interaction data for all major model organism species and humans. It allows users to investigate the function of individual genes and pathways, as well as to analyze the properties of large biological networks. This database is curated with an automated random re-curation procedure.
Allows searching, visualizing and retrieving of integrated interaction data. CPDB is an integrative interaction database that gathers molecular interaction data integrated from 32 different public repositories and provides a set of computational methods and visualization tools to explore these data. Its applications comprise over-representation analysis to characterize diverse sets of molecules, gene set enrichment analysis (GSEA) and identification of upstream regulators spanning various biological context. It is also used as a database by other tools, for instance by Cytoscape and Chipster.
Provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles; data from high-throughput experiments is excluded.
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 stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
Provides access to experimentally derived information about the human proteome including protein–protein interactions (PPIs), post-translational modifications (PTMs) and tissue expression. HPRD is an integrated knowledgebase for genomic and proteomic investigators. The database also includes (i) PhosphoMotif Finder that contains known kinase/phosphatase substrate and binding motifs, (ii) links to a signaling pathway resource called NetPath, (iii) a distributed annotation system, called Human Proteinpedia for enhanced community participation and allows the use of BLAST for querying mRNA/protein data.
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 PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.
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 with exhaustive information on structures of the same or homologous proteins in bound and unbound states.