BetaDock: Shape-Priority Docking Method Based on Beta-Complex

Abstract

This paper presents an approach and a software. Beta Dock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the beta-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the beta-complex corresponding to water molecule is computed. Then, the boundary of the beta-complex defines the beta-shape which has the complete proximity information among all atoms on the receptor boundary. From the beta-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that Beta Dock is superior to a popular docking software AutoDock 4.