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.
Gathers information related to both known and predicted protein-protein interactions (PPIs). STRING is a repository displaying information about physical and functional associations of over 9 000 000 proteins from more than 2 000 organisms. Searches can be made by protein name, sequence or through user-imported files. The repository also provides numerous datasets freely downloadable, a panel allowing registered users to save their researches and an additional database dealing with virus-virus and virus-host interactions.
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 levels and allowing their analysis and visualization as networks. This method is focused solely on the generation and delivery of unified compendiums of known and experimentally proven protein–protein physical interactions (PPIs).
Reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. BioPlex structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally-related proteins. This tool can be used to reveal interactions of biological or clinical significance. The BioPlex (biophysical interactions of ORFeome-based complexes) network is the result of creating thousands of cell lines with each expressing a tagged version of a protein from the ORFeome collection.
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 have to specify the type of record, and the dataset which they want interrogate. Different types of information are available about protein, interaction, and network graphic.
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 completely remodeled database structure, which offers more efficient data exploration and analysis, and is characterized by entries with a richer annotation. MINT includes, as an integrated addition, HomoMINT, a database of interactions between human proteins inferred from experiments with ortholog proteins in model organisms.
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.
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 protein-coding genes. This approach is based on utilization of yeast two-hybrid (Y2H) as the primary screening method.
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 biological pathways. It is constructed as a free database and analysis server to enable users to rapidly search and retrieve summarized EMT-related genes.
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 protein-protein interaction (PPI) networks, signal-gene protein interaction pathways and Boolean networks. Higher degree neighbourhood networks can be visualized to determine critical hubs and crosstalk associations between interacting partners. This resource may also be used to design directed experiments that provide better insight and reveal potential druggable targets.
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.
Defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK is a 3D database system that combines the PFAM domain classification with coordinate data from the Protein Data Bank (PDB) to analyse the spatial arrangements of domain-domain interactions (DDIs) and domain-peptide interactions (DPIs) by Pfam family, and to propose structural templates for protein docking. It can also find DDIs involving structurally similar Pfam domains to the query domains using pre-calculated Pfam neighbour lists.
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 perturbations in such networks can explain phenotypes and human disease.
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 multiple resources. The database collates experimental evidences from any species for which interaction data is available. It is curated from direct submissions or peer-reviewed journals.
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.
Provides an integrated human protein-protein interaction (PPI) network. InWeb_IM is composed of more than 600 000 interactions sourced from eight databases and spanning 87 per cent of reviewed human UniProt IDs. Each interaction is associated with an initial score based on a number of metrics. It gathers curve of the enrichment of the gold-standard interactions as a function of the rank based on the initial score.
Covers interactions established by extracellular proteins and polysaccharides. MatrixDB contains protein-protein interactions (PPIs) and also protein-glycosaminoglycan interactions. It can be employed to construct interaction networks of extracellular proteins, glycosaminoglycans, proteoglycans, basement membrane or physiological process. This database offers about 1 000 interactions supported by over 1 200 experiments, which have been manually curated.
Provides an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. PINA includes a quarterly updated, nonredundant database based on integration of data from six public protein-protein integration (PPI) databases: IntAct, MINT, BioGRID, DIP, HPRD and MIPS MPact. This application provides capabilities allowing to construct PPIs networks, such as queries for single proteins, a list of proteins, a list of protein pairs or two lists of proteins.
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, unique co-complex interactions and unique 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 original publications and, wherever necessary, data were re-confirmed by contacting the authors. It is organized in three hyperlinked flat files. The database offers a search engine that enables the user to make research through all fields of the flat files.