Comparison of three nature inspired molecular docking algorithms

Abstract

Molecular docking uses different methods to generate and evaluate the binding between a receptor and a ligand. Three nature-inspired docking programs are compared on a test set of 65 receptor-ligand pairs. AutoDock uses a genetic algorithm inspired by the process of natural selection; PSOVina2LS uses the particle swarm optimisation method, based on the behaviour of animal flocks and PLANTS uses an algorithm based on ant colonies. Using the default parameters, PSOVina2LS achieved the best performance with respect to time required and docking accuracy, followed by PLANTS and, with a large gap, AutoDock. However, all the programs exhibited difficulties with redocking of ligands with more than ten rotable bonds.