Abstract
BackgroundMost proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.DescriptionWe introduce a large-scale protein domain interaction interface database called InterPare . It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website.ConclusionInterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces.
Highlights
Most proteins function by interacting with other molecules
InterPare contains 10,583, 10,431, and 11,010 Protein Data Bank (PDB) entries that have been identified as containing interacting interfaces according to geometric distance, accessible surface area (ASA), and the Voronoi diagram methods respectively
PFrigouterien s2tructure with respect to their geometrical region Protein structure with respect to their geometrical region. (a) Schematic diagram representing the interior, interface, and surface of longitudinal section of a protein domain. (b) An example of a 3D structure (SCOP id: d1a25a_) which corresponds to a schematic diagram (a)
Summary
InterPare is an open and public database server for protein interaction interface information. It contains large-scale interface data for proteins whose 3D-structures are known. At this moment, there are 10,583, 10,431, and 11,010 PDB entries whose domain interaction interfaces have been identified according to geometric distance, ASA, and Voronoi diagram methods, respectively. There are 10,583, 10,431, and 11,010 PDB entries whose domain interaction interfaces have been identified according to geometric distance, ASA, and Voronoi diagram methods, respectively These interfaces are based on protein domains which are from the SCOP database. DSK supervised the development of Voronoi diagram method.
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