Improving differential evolution accuracy for flexible ligand docking using a multi-solution strategy

Authors:
Camila S. de Magalhães;Carlos Henrique dos S. Barbosa;Diogo M. Almeida;Laurent E. Dardenne
Affiliations:
Departamento de Matemática, Universidade Federal Rural do Rio de Janeiro - UFRRJ, Rio de Janeiro, Brazil,Departamento de Mecânica, Laboratório Nacional de Computacão Cientí ...;Departamento de Matemática, Universidade Federal Rural do Rio de Janeiro - UFRRJ, Rio de Janeiro, Brazil,Departamento de Mecânica, Laboratório Nacional de Computacão Cientí ...;Departamento de Matemática, Universidade Federal Rural do Rio de Janeiro - UFRRJ, Rio de Janeiro, Brazil,Departamento de Mecânica, Laboratório Nacional de Computacão Cientí ...;Departamento de Matemática, Universidade Federal Rural do Rio de Janeiro - UFRRJ, Rio de Janeiro, Brazil,Departamento de Mecânica, Laboratório Nacional de Computacão Cientí ...
Venue:
IDEAL'12 Proceedings of the 13th international conference on Intelligent Data Engineering and Automated Learning
Year:
2012

Citing 3
Cited 0

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Abstract

Docking of small ligand molecules in protein active sites is a very important and challenging problem in the structure-based drug design field. In this work we propose a Differential Evolution algorithm in conjunction with a multi-solution strategy for the flexible ligand docking problem. The proposed algorithm is evaluated on five highly flexible HIV-1 protease ligands, with known three-dimensional structures, having up to 19 conformational degrees of freedom. The docking results and comparison with classic Differential Evolution algorithm indicate that the incorporation of a multi-solution strategy in Differential Evolution algorithms is very promising and can significantly improve molecular docking accuracy.