Multi-scale optimization model and algorithm for computer-aided molecular docking

A multi-scale optimization model and algorithm are presented into molecular docking problem. In this model, a concept of residue groups based on induced-fit is introduced to the refined docking design. An adaptive evolution algorithm is developed to address the optimization problem. Multi-population evolution and information entropy-based searching techniques with narrowing space are employed in the method, making the efficiency of the genetic evolution very high. A new docking program that accounts for protein flexibility has also been developed. Docking results indicate that the method can be efficiently employed in molecular drug design.