Most 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. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.
Here, we introduce two web-based services for protein interactomics study: PSlbase and InterPare. 1) PSlbase (http://psimap.org or http://psibase.kaist.ac.kr) is a database and file server for protein structural interaction information. It provides a map to view genomic-scale protein interaction at protein family or superfamily level. 2) InterPare (http://interpare.kaist.ac.kr or http://interpare.net) is a large-scale protein domain interaction interface database. It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. Three methods have been used to detect interacting interfaces: 1) the geometric distance method, 2) Accessible Surface Area (ASA) method, and 3) the Voronoi diagram method.
By using PSlbase and InterPare users can retrieve 1) domain-domain and protein-protein interaction information from proteins whose 3D-structures are identified, 2) a protein interaction map and its viewer at protein superfamily and family levels, 3) protein interior, surface, and interaction interface views, 4) atom coordinate files that belong to interface, surface, and interior regions. They also provide 1) structural domain prediction tools for possible interactions by detecting homologous matches in PDB from query sequences, and 2) statistics such as the amino acid propensities of queried protein according to its interior, surface and interface region. We believe that PSlbase and InterPare can be a useful resource in the fields of structure biology, bioinformatics, and drug discovery.