Journal
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
Volume 32, Issue 6, Pages 789-803Publisher
SAGE PUBLICATIONS LTD
DOI: 10.1177/1094342017697471
Keywords
Drug discovery; virtual screening; molecular docking; high performance computing; metaheuristics; heterogeneous computing
Categories
Funding
- Fundacion Seneca, Agencia Regional de Ciencia y Tecnologia, Region de Murcia [18946/JLI/13]
- Spanish MEC
- European Commission FEDER [TIN2015-66972-C5-3-R, TIN2016-78799-P]
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Virtual screening through molecular docking can be translated into an optimization problem, which can be tackled with metaheuristic methods. The interaction between two chemical compounds (typically a protein, enzyme or receptor, and a small molecule, or ligand) is calculated by using highly computationally demanding scoring functions that are computed at several binding spots located throughout the protein surface. This paper introduces METADOCK, a novel molecular docking methodology based on parameterized and parallel metaheuristics and designed to leverage heterogeneous computers based on heterogeneous architectures. The application decides the optimization technique at running time by setting a configuration schema. Our proposed solution finds a good workload balance via dynamic assignment of jobs to heterogeneous resources which perform independent metaheuristic executions when computing different molecular interactions required by the scoring functions in use. A cooperative scheduling of jobs optimizes the quality of the solution and the overall performance of the simulation, so opening a new path for further developments of virtual screening methods on high-performance contemporary heterogeneous platforms.
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