Multi-objective ligand-protein docking with particle swarm optimizers
In the last years, particle swarm optimizers have emerged as prominent search methods to solve the molecular docking problem. A new approach to address this problem consists in a multi-objective formulation, minimizing the intermolecular energy and the Root Mean Square Deviation (RMSD) between the a...
| Autores: | , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión enviada para evaluación y publicación |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Universidad de Sevilla (US) |
| Repositorio: | idUS. Depósito de Investigación de la Universidad de Sevilla |
| OAI Identifier: | oai:idus.us.es:11441/108832 |
| Acceso en línea: | https://hdl.handle.net/11441/108832 https://doi.org/10.1016/j.swevo.2018.05.007 |
| Access Level: | acceso abierto |
| Palabra clave: | Multi-objective optimization Particle Swarm Optimization Molecular Docking Archiving Strategies Algorithm Comparison |
| Sumario: | In the last years, particle swarm optimizers have emerged as prominent search methods to solve the molecular docking problem. A new approach to address this problem consists in a multi-objective formulation, minimizing the intermolecular energy and the Root Mean Square Deviation (RMSD) between the atom coordinates of the co-crystallized and the predicted ligand conformations. In this paper, we analyze the performance of a set of multi-objective particle swarm optimization variants based on different archiving and leader selection strategies, in the scope of molecular docking. The conducted experiments involve a large set of 75 molecular instances from the Protein Data Bank database (PDB) characterized by different sizes of HIV-protease inhibitors. The main motivation is to provide molecular biologists with unbiased conclusions concerning which algorithmic variant should be used in drug discovery. Our study confirms that the multi-objective particle swarm algorithms SMPSOhv and MPSO/D show the best overall performance. An analysis of the resulting molecular ligand conformations, in terms of binding site and molecular interactions, is also performed to validate the solutions found, from a biological point of view. |
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