A structural informatics approach to mine kinase knowledge bases.
In this paper, we describe a combination of structural informatics approaches developed to mine data extracted from existing structure knowledge bases (Protein Data Bank and the GVK database) with a focus on kinase ATP-binding site data. In contrast to existing systems that retrieve and analyze protein structures, our techniques are centered on a database of ligand-bound geometries in relation to residues lining the binding site and transparent access to ligand-based SAR data. We illustrate the systems in the context of the Abelson kinase and related inhibitor structures.
Brooijmans
Natasja
N
Computational Chemistry and Cheminformatics, Wyeth Research, 401 North Middletown Road, Pearl River, NY 10965, USA.
Mobilio
Dominick
D
Walker
Gary
G
Nilakantan
Ramaswamy
R
Denny
Rajiah A
RA
Feyfant
Eric
E
Diller
David
D
Bikker
Jack
J
Humblet
Christine
C
D000818:Animals; D018360:Crystallography, X-Ray; D006801:Humans; D048088:Informatics / Q000379:methods* / Q000639:trends; D051188:Knowledge Bases; D015394:Molecular Structure; D011494:Protein Kinases / Q000737:chemistry* / Q000235:genetics; D013329:Structure-Activity Relationship
D011494:Protein Kinases