A parallel evolutionary approach to the molecular docking problem

Daniel Espinosa-Galindo; Jesús A. Fernández-Flores; Inés A. Almanza-Román; Rosaura Palma-Orozco; J. Orge L. Rosas-Trigueros

doi:10.1007/978-3-319-57972-6_19

A parallel evolutionary approach to the molecular docking problem

Daniel Espinosa-Galindo, Jesús A. Fernández-Flores, Inés A. Almanza-Román, Rosaura Palma-Orozco, J. Orge L. Rosas-Trigueros

Escuela Superior de Cómputo (ESCOM)

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

The ligand-protein molecular docking is an unsolved problem in Bioinformatics consisting in determining the way in which two such molecules bind in nature, depending on their structure and interaction. The solution of this problem is one of the core aims of Bioinformatics and the basis for the rational drug design process. Through the use of evolutionary and parallelization techniques, a new approach is presented, consisting of a threaded implementation of an island model genetic algorithm. The results show a mixed outcome, with an aided search version achieving quick and accurate predictions, while the more ambitious free search proposal still does not produce acceptable results. Additional advantages of the software obtained are cross-platform nature, reasonable performance on average consumer hardware and ease of use.

Original language	English
Title of host publication	High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers
Editors	Carlos Jaime Barrios Hernandez, Isidoro Gitler, Jaime Klapp
Publisher	Springer Verlag
Pages	257-268
Number of pages	12
ISBN (Print)	9783319579719
DOIs	https://doi.org/10.1007/978-3-319-57972-6_19
State	Published - 2017
Event	3rd Latin American Conference on High Performance Computing, CARLA 2016 - Mexico City, Mexico Duration: 29 Aug 2016 → 2 Sep 2016

Publication series

Name	Communications in Computer and Information Science
Volume	697
ISSN (Print)	1865-0929

Conference

Conference	3rd Latin American Conference on High Performance Computing, CARLA 2016
Country/Territory	Mexico
City	Mexico City
Period	29/08/16 → 2/09/16

Keywords

Bioinformatics
Docking
Evolutionary Computing
Parallel Computing

Access to Document

10.1007/978-3-319-57972-6_19

Cite this

Espinosa-Galindo, D., Fernández-Flores, J. A., Almanza-Román, I. A., Palma-Orozco, R., & Rosas-Trigueros, J. O. L. (2017). A parallel evolutionary approach to the molecular docking problem. In C. J. Barrios Hernandez, I. Gitler, & J. Klapp (Eds.), High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers (pp. 257-268). (Communications in Computer and Information Science; Vol. 697). Springer Verlag. https://doi.org/10.1007/978-3-319-57972-6_19

Espinosa-Galindo, Daniel ; Fernández-Flores, Jesús A. ; Almanza-Román, Inés A. et al. / A parallel evolutionary approach to the molecular docking problem. High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers. editor / Carlos Jaime Barrios Hernandez ; Isidoro Gitler ; Jaime Klapp. Springer Verlag, 2017. pp. 257-268 (Communications in Computer and Information Science).

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abstract = "The ligand-protein molecular docking is an unsolved problem in Bioinformatics consisting in determining the way in which two such molecules bind in nature, depending on their structure and interaction. The solution of this problem is one of the core aims of Bioinformatics and the basis for the rational drug design process. Through the use of evolutionary and parallelization techniques, a new approach is presented, consisting of a threaded implementation of an island model genetic algorithm. The results show a mixed outcome, with an aided search version achieving quick and accurate predictions, while the more ambitious free search proposal still does not produce acceptable results. Additional advantages of the software obtained are cross-platform nature, reasonable performance on average consumer hardware and ease of use.",

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Espinosa-Galindo, D, Fernández-Flores, JA, Almanza-Román, IA, Palma-Orozco, R & Rosas-Trigueros, JOL 2017, A parallel evolutionary approach to the molecular docking problem. in CJ Barrios Hernandez, I Gitler & J Klapp (eds), High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers. Communications in Computer and Information Science, vol. 697, Springer Verlag, pp. 257-268, 3rd Latin American Conference on High Performance Computing, CARLA 2016, Mexico City, Mexico, 29/08/16. https://doi.org/10.1007/978-3-319-57972-6_19

A parallel evolutionary approach to the molecular docking problem. / Espinosa-Galindo, Daniel; Fernández-Flores, Jesús A.; Almanza-Román, Inés A. et al.
High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers. ed. / Carlos Jaime Barrios Hernandez; Isidoro Gitler; Jaime Klapp. Springer Verlag, 2017. p. 257-268 (Communications in Computer and Information Science; Vol. 697).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Espinosa-Galindo, Daniel

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AU - Almanza-Román, Inés A.

AU - Palma-Orozco, Rosaura

AU - Rosas-Trigueros, J. Orge L.

N1 - Publisher Copyright: © Springer International Publishing AG 2017.

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AB - The ligand-protein molecular docking is an unsolved problem in Bioinformatics consisting in determining the way in which two such molecules bind in nature, depending on their structure and interaction. The solution of this problem is one of the core aims of Bioinformatics and the basis for the rational drug design process. Through the use of evolutionary and parallelization techniques, a new approach is presented, consisting of a threaded implementation of an island model genetic algorithm. The results show a mixed outcome, with an aided search version achieving quick and accurate predictions, while the more ambitious free search proposal still does not produce acceptable results. Additional advantages of the software obtained are cross-platform nature, reasonable performance on average consumer hardware and ease of use.

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Espinosa-Galindo D, Fernández-Flores JA, Almanza-Román IA, Palma-Orozco R , Rosas-Trigueros JOL. A parallel evolutionary approach to the molecular docking problem. In Barrios Hernandez CJ, Gitler I, Klapp J, editors, High Performance Computing - 3rd Latin American Conference, CARLA 2016, Revised Selected Papers. Springer Verlag. 2017. p. 257-268. (Communications in Computer and Information Science). doi: 10.1007/978-3-319-57972-6_19

A parallel evolutionary approach to the molecular docking problem

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Keywords

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