Finding the optimal parameter values for any computer program with adjustable parameters can be very time consuming. In this paper, we introduce the use of the Plackett-Burman and the central composite designs with the aid of the partial least squares method to tackle this problem. Using DOCK3.5 as a test case, we also show a four-step procedure for sequential docking utilizing two parameter sets, both effecting a different level of accuracy. The DOCK parameter values were refined for protein kinase C regulatory domain yielding an orientation at the global "energy" minimum, which is in very good agreement with the experimental 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.
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