Molecular docking method considering protein flexibility

Molecular structural optimization is an invaluable tool in computer-aided molecular design. A new flexible docking optimization model based on induced-fit interaction is proposed. In the model, a concept of residue groups is introduced to describe the protein movement approximately and the movement of ligand is described by the translation, votation and torsion motions. A new iteration scheme in conjunction with the k-means clustering algorithm and genetic algorithm is developed to solve the optimization model for the molecular docking. Multi-population genetic strategy and entropy-based searching technique with narrowing down space are employed in the method, making the efficiency of genetic evolution very high. A new docking program FlexGAsDock considering the protein flexibility has been developed. The docking results show that the method can be used in the drug molecular design efficiently.