Jp. Salo et al., PARAMETER REFINEMENT FOR MOLECULAR DOCKING, Journal of chemical information and computer sciences, 38(5), 1998, pp. 832-839
Citations number
40
Categorie Soggetti
Computer Science Interdisciplinary Applications","Computer Science Information Systems","Computer Science Interdisciplinary Applications",Chemistry,"Computer Science Information Systems
Finding the optimal parameter values for any computer program with adj
ustable parameters can be very time consuming. In this paper, we intro
duce the use of the Plackett-Burman and the central composite designs
with the aid of the partial least squares method to tackle this proble
m. Using DOCK3.5 as a test case, we also show a four-step procedure fo
r sequential docking utilizing two parameter sets, both effecting a di
fferent level of accuracy. The DOCK parameter values were refined for
protein kinase C regulatory domain yielding an orientation at the glob
al ''energy'' minimum, which is in very good agreement with the experi
mental protein kinase C regulatory domain-phorbol 13-acetate complex.
The scheme is now being used for screening molecular databases to find
putative protein kinase C inhibitors.