PDBSite DATABASE AND PDBSiteScan TOOL: RECOGNITION OF FUNCTIONAL SITES IN PROTEIN 3d STRUCTURE AND TEMPLATE-BASED DOCKING
Novosibirsk State · 2006
*SUMMARY Motivation: Recognition of functional sites in proteins is a direct computational approach providing a better understanding of protein biological and biochemical functions. Use of information about the protein spatial structure broadens our understanding of the structural organization of the functional sites, providing their recognition in the most efficient and accurate manner. Results: We developed a new version for the PDBSite database that contains 3d templates of various protein functional sites (posttranslational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and proteinRNA interactions) and also a new version of the PDBSiteScan tool ensuring the recognition of functional sites using 3d templates and the creation of molecular proteinligand complexes relying on template based docking. The number of functional and drug binding sites stored in PDBSite was considerably increased, also, PDBSite was integrated with the other established molecular-biological databases. Availability: http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/, http://wwwmgs.bionet. nsc.ru/mgs/systems/fastprot/pdbsitescan.html.