The Drug discovery on grid project is aimed at developing a platform for drug discovery, on which various calculations and simulations are effectively executed at high speed. For storing and retrieving calculated and experimental information, the drug, markup language database is an extension of the chemical markup language database with appropriate figures as indicated. Before the docking of a drug molecule with its target receptor, an extensive conformational search of the drug molecule is carried out for defining the bioactive conformation. The conformational search is carried out for a series of molecules selected from the database, where information on the two-dimensional structure of molecules is stored. Then all the low energy conformers obtained in the previous procedure are subjected to the docking analysis. There are three methods for evaluating the docking energy; the fragment molecular orbital , the replica exchange molecular dynamics , and the empirical scoring function based on the energy obtained from the force field calculation and indexes of three-dimensional complementary structure between a drug and its target protein. The chapter studies CONFLEX that has been recognized as one of the most efficient conformational space search programs. The types of CONFLEX and its application to peptide folding are studied along with flowcharts. Hence, computational techniques, such as parallel computing and grid will enable to probe the drug-receptor mediated phenomenon directly.
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