METADOCK: A parallel metaheuristic schema for virtual screening methods. (November 2018)

• Record Type: Journal Article
• Authors: Imbernón, Baldomero; Cecilia, José M; Pérez-Sánchez, Horacio; Giménez, Domingo
• Other Names: Balaji Pavan guest-editor.; Leung Kai-Cheung guest-editor.; Huang Zhiyi guest-editor.; García-Blas Javier guest-editor.; Brown Christopher guest-editor.
• Is Part Of: International journal of high performance computing applications. Volume 32:Number 6(2018)
• Page Start: 789
• Page End: 803
• Publication Date: 2018-11
• Subjects: Drug discovery -- virtual screening -- molecular docking -- high performance computing -- metaheuristics -- heterogeneous computing; High performance computing -- Periodicals; Supercomputers -- Periodicals; 004.1105
• DOI: 10.1177/1094342017697471
• Languages: English
• ISSNs: 1094-3420

Abstract

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.