A force fields-based multi-scale docking method in drug molecular design

A force fields-based multi-scale docking method is proposed in this paper. Molecular docking problem has been divided into three sub problems: rigid-rigid phase, flexible-flexible phase and flexible-rigid phase. Residue groups of protein have been adopted to describe the conformation of protein. K-mean clustering algorithm and genetic algorithm have been developed to solve the optimization problem. A new docking program, which relies on calculated non-bonded interaction terms between protein and ligand atoms based on standard force fields, has been developed. In comparison with other docking methods, the docking method has significant improvement in docking accuracy.