Minimum Population Search, an Application to Molecular Docking

Gecontec: Revista Internacional de Gestión del Conocimiento y la Tecnología, Vol. 2 (3) 2014

16 Pages Posted: 24 Sep 2014

See all articles by Antonio Bolufé-Röhler

Antonio Bolufé-Röhler

Universidad de la Habana

Alex Coto-Santiesteban

Universidad de la Habana

Marta Rosa-Soto

Institute of Cybernetics, Mathematical and Physical (ICIMAF)

Stephen Chen

York University

Date Written: September 23, 2014

Abstract

Computer modeling of protein-ligand interactions is one of the most important phases in a drug design process. Part of the process involves the optimization of highly multi-modal objective (scoring) functions. This research presents the Minimum Population Search heuristic as an alternative for solving these global unconstrained optimization problems. To determine the effectiveness of Minimum Population Search, a comparison with seven state-of-the-art search heuristics is performed. Being specifically designed for the optimization of large scale multi-modal problems, Minimum Population Search achieves excellent results on all of the tested complexes, especially when the amount of available function evaluations is strongly reduced. A first step is also made toward the design of hybrid algorithms based on the exploratory power of Minimum Population Search. Computational results show that hybridization leads to a further improvement in performance.

Keywords: Minimum Population Search; Molecular Docking; Heuristic Algorithms; Optimization; Multi-modality

Suggested Citation

Bolufé-Röhler, Antonio and Coto-Santiesteban, Alex and Rosa-Soto, Marta and Chen, Stephen, Minimum Population Search, an Application to Molecular Docking (September 23, 2014). Gecontec: Revista Internacional de Gestión del Conocimiento y la Tecnología, Vol. 2 (3) 2014 . Available at SSRN: https://ssrn.com/abstract=2500219

Antonio Bolufé-Röhler (Contact Author)

Universidad de la Habana ( email )

San Lazaro
Havana
Cuba

Alex Coto-Santiesteban

Universidad de la Habana ( email )

Colina Universitaria
Havana
Cuba

Marta Rosa-Soto

Institute of Cybernetics, Mathematical and Physical (ICIMAF) ( email )

Calle E, No. 309, Vedado,
La Habana, Ciudad Habana 10400
Cuba

Stephen Chen

York University ( email )

4700 Keele Street
Toronto, Ontario M3J 1P3
Canada

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