title: A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.
abstract: The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.
authors.affiliation: Department of Computational Chemistry and Cheminformatics, Wyeth Research, 401 N. Middletown Rd., Pearl River, NY 10965, USA. dom@dmobilio.com
authors.forename: Dominick
authors.initials: D
authors.lastname: Mobilio
authors.forename: Gary
authors.initials: G
authors.lastname: Walker
authors.forename: Natasja
authors.initials: N
authors.lastname: Brooijmans
authors.forename: Ramaswamy
authors.initials: R
authors.lastname: Nilakantan
authors.forename: R Aldrin
authors.initials: RA
authors.lastname: Denny
authors.forename: Jason
authors.initials: J
authors.lastname: Dejoannis
authors.forename: Eric
authors.initials: E
authors.lastname: Feyfant
authors.forename: Rupesh K
authors.initials: RK
authors.lastname: Kowticwar
authors.forename: Jyoti
authors.initials: J
authors.lastname: Mankala
authors.forename: Satish
authors.initials: S
authors.lastname: Palli
authors.forename: Sairam
authors.initials: S
authors.lastname: Punyamantula
authors.forename: Maneesh
authors.initials: M
authors.lastname: Tatipally
authors.forename: Reji K
authors.initials: RK
authors.lastname: John
authors.forename: Christine
authors.initials: C
authors.lastname: Humblet
mesh_terms: D030562:Databases, Protein; D015195:Drug Design; D051188:Knowledge Bases; D020782:Matrix Metalloproteinases / Q000737:chemistry; D011494:Protein Kinases / Q000737:chemistry
chemical_list: D011494:Protein Kinases; D020782:Matrix Metalloproteinases