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; PSOVina^2LS 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, PSOVina^2LS 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.

DOI: 10.1504/IJBIC.2021.113362

International Journal of Bio-Inspired Computation, 2021 Vol.17 No.1, pp.34 - 41

Accepted: 29 Jul 2020
Published online: 01 Mar 2021 *

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