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On the efficiency of local search methods for the molecular docking problem

Jorge Tavares 1 Salma Masmoudi El-Ghazali Talbi 2
2 DOLPHIN - Parallel Cooperative Multi-criteria Optimization
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : Evolutionary approaches to molecular docking typically hybridize with local search methods, more specifically, the Solis-Wet method. However, some studies indicated that local search methods might not be very helpful in the context of molecular docking. An evolutionary algorithm with proper genetic operators can perform equally well or even outperform hybrid evolutionary approaches. We show that this is dependent on the type of local search method. We also propose an evolutionary algorithm which uses the L-BFGS method as local search. Results demonstrate that this hybrid evolutionary outperforms previous approaches and is better suited to serve as a basis for evolutionary docking methods.
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https://hal.inria.fr/hal-00837528
Contributor : Talbi El-Ghazali Connect in order to contact the contributor
Submitted on : Saturday, June 22, 2013 - 6:04:30 PM
Last modification on : Thursday, January 20, 2022 - 5:27:53 PM

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Jorge Tavares, Salma Masmoudi, El-Ghazali Talbi. On the efficiency of local search methods for the molecular docking problem. EvoBio 2009 - 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Apr 2009, Tubingen, Germany. pp.104-115, ⟨10.1007/978-3-642-01184-9_10⟩. ⟨hal-00837528⟩

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