Vivienne Baillie Gerritsen, Swiss Institute of Bioinformatics, Geneva, Switzerland
Amos Bairoch, Swiss Institute of Bioinformatics, Geneva, Switzerland
Published online: September 2005
DOI: 10.1038/npg.els.0005251
An abundance of protein databases are available, dealing with fields as diverse as protein sequences, protein domains, posttranslational modifications and protein–protein interactions. Such resources are crucial to proteomics research.
Keywords: protein; knowledgebase; proteomics; proteome; database
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| Web Links | |
| ePath The ExPASy list of Biomolecular servers. This site lists the major (over one thousand!) databases of interest relative to proteomic research http://www.expasy.org/alinks.html | |
| ePath BIND. The Biomolecular Interaction Network Database stores full descriptions of interactions, molecular complexes and pathways, among which are protein–protein interactions http://bind.mshri.on.ca/ | |
| ePath BRENDA. The main collection of enzyme functional data available to the scientific community, maintained and developed at the Institute of Biochemistry at the University of Cologne http://www.brenda.uni-koeln.de/ | |
| ePath CATH. A hierarchical domain classification of protein structures derived from PDB (see below) http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html | |
| ePath DbSNP. The Single Nucleotide Polymorphism database is a repository of all the genetic variations which are discovered as the human genome is being deciphere http://www.ncbi.nlm.nih.gov/SNP | |
| ePath DIP. The Database of Interacting Proteins is curated both manually by expert curators and automatically. The DIP database provides a comprehensive and integrated tool for browsing and extracting information on protein–protein interactions http://dip.doe-mbi.ucla.edu/ | |
| ePath ENZYME. An enzyme nomenclature database based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) http://us.expasy.org/enzyme/ | |
| ePath GlycoSuiteDB. A database of glycoprotein glycan structures derived from the scientific literature. Regarding proteins, when the glycan structures are known to be attached to a specific protein, direct links are made to Swiss-Prot and TrEMBL databases (see below) http://www.glycosuite.com/ | |
| ePath GPCRDB. An information system, which collects and disseminates data related to the G-protein-coupled receptor http://www.gpcr.org/7tm | |
| ePath HGMD. The Human Gene Mutation Database is a comprehensive database of gene lesions underlying human inherited disease http://www.hgmd.org/ | |
| ePath HGVS. The Human Genome Variation Society was created to promote the discovery and free publication of information on the variations in human genes by fostering a central repository for such variations http://www.hgvs.org/ | |
| ePath IMGT. The international ImMunoGeneTics database is a high-quality integrated information system that specializes in immunoglobulins, T cell receptors and major histocompatibility complex molecules of all vertebrate species http://imgt.cines.fr:8104/ | |
| ePath InterPro. An integrated documentation resource for protein families, domains and functional sites, which was developed to rationalize the complementary efforts of the individual protein signature database projects that form the InterPro core (see Table 1) http://www.ebi.ac.uk/interpro/ | |
| ePath KEGG. The Kyoto Encyclopedia of Genes and Genomes strives to computerize the current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes http://www.genome.ad.jp/kegg/ | |
| ePath MEROPS. Provides data on individual proteases, protease families and also clans into which the families are grouped http://merops.iapc.bbsrc.ac.uk/ | |
| ePath MINT. The Molecular Interactions database. Stores functional interactions between biological molecules. http://cbm.bio.uni.oma2.it/mint/ | |
| ePath OMIM. The Online Mendelian Inheritance in Man database is a collection of human genes and genetic disorders maintained by the McKusick–Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and the National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD). The database offers a wealth of textual information provided in each entry, some of which can be useful in the context of protein studies http://www.ncbi.nlm.nih.gov/omim/ | |
| ePath PDB. The Protein Data Bank is a collection of 3D structures of proteins, nucleic acids and other biological macromolecules. PDB is a resource of critical importance in the discovery of new pharmacological agents, new catalysts, new biomaterials and possibly nanodevices http://www.rcsb.org/pdb/ | |
| ePath SCOP. Provides a detailed and comprehensive description of the structural and evolutionary relationships between proteins whose structure is known http://scop.mrc-lmb.cam.ac.uk/scop/ | |
| ePath Swiss-2Dpage. Contains 2D-PAGE and SDS PAGE reference maps and information on identified proteins from a variety of human biological samples. It is maintained collaboratively by the Central Clinical Chemistry Laboratory of the Geneva University Hospital and the Swiss Institute of Bioinformatics http://www.expasy.org/ch2d/ | |
| ePath Swiss-Prot. A non-redundant curated protein knowledge resource that provides a high level of annotation. Besides the stark protein sequence, a Swiss-Prot entry offers the description of the function of a protein, its domain structure, posttranslational modifications, variants and links to other databases http://www.expasy.org/sprot | |
| ePath TrEMBL. Consists of computer-annotated entries in Swiss-Prot format derived from the translation of coding sequences in the European Molecular Biology Laboratory nucleotide sequence database. Hence TrEMBL entries are preliminary Swiss-Prot entries that have not yet been manually annotated http://www.ebi.ac.uk/swissprot | |
| ePath World-2Dpage. A complete index of 2D-PAGE databases and services http://www.expasy.org/ch2d/2d-index.html | |
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