A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.
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.
Mobilio
Dominick
D
Department of Computational Chemistry and Cheminformatics, Wyeth Research, 401 N. Middletown Rd., Pearl River, NY 10965, USA. dom@dmobilio.com
Walker
Gary
G
Brooijmans
Natasja
N
Nilakantan
Ramaswamy
R
Denny
R Aldrin
RA
Dejoannis
Jason
J
Feyfant
Eric
E
Kowticwar
Rupesh K
RK
Mankala
Jyoti
J
Palli
Satish
S
Punyamantula
Sairam
S
Tatipally
Maneesh
M
John
Reji K
RK
Humblet
Christine
C
D030562:Databases, Protein; D015195:Drug Design; D051188:Knowledge Bases; D020782:Matrix Metalloproteinases / Q000737:chemistry; D011494:Protein Kinases / Q000737:chemistry
D011494:Protein Kinases; D020782:Matrix Metalloproteinases