Research on Rigid Molecular Docking of HIV-1 Proease and Benzamidine by the Generaized Stimulated Annealing Algorithm
Zhang You · Acta Scientiarum Naturalium Universitatis Neimongol · 2001
The generalized stimulated annealing algorithm is a new global optimization algorithm, which is efficient when the freedom degrees of the objective function is not very large. We applied the algorithm to molecular docking problems. The algorithm is applied to the docking of several simple model molecules and the docking between the benzamidine and HIV 1 protease.The theoretical result is consistent with the crystal structure data with only 0.03 nm root mean squared deviation. The results show that the algorithm can be used to find the energetically most favored configurations of docking molecules.