METADOCK: A parallel metaheuristic schema for virtual screening methods
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Author/sImbernón Tudela, Baldomero; Cecilia Canales, José María; Pérez Sánchez, Horacio; Giménez Cánovas, Domingo
Discipline/sIngeniería, Industria y Construcción
High Performance Computing
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 sched...