Title: Comparison of three nature inspired molecular docking algorithms
Authors: Petra Čechová; Martin Kubala
Addresses: Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic; Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic ' Department of Experimental Physics, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic; Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
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.
Keywords: molecular docking; redocking study; genetic algorithm; particle swarm optimisation; PSO; ant colony optimisation; ACO.
International Journal of Bio-Inspired Computation, 2021 Vol.17 No.1, pp.34 - 41
Accepted: 29 Jul 2020
Published online: 01 Mar 2021 *