Title
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
Date Issued
21 September 2020
Access level
open access
Resource Type
conference paper
Author(s)
Legrand S.
Scheinberg A.
Tillack A.F.
Thavappiragasam M.
Vermaas J.V.
Agarwal R.
Larkin J.
Poole D.
Santos-Martins D.
Koch A.
Forli S.
Hernandez O.
Smith J.C.
Sedova A.
Tu Darmstadt
Publisher(s)
Association for Computing Machinery, Inc
Abstract
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-Throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.
Language
English
OCDE Knowledge area
Farmacología, Farmacia Bioinformática
Scopus EID
2-s2.0-85096991107
ISBN
9781450379649
Conference
Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020
Sponsor(s)
Funding text This research was sponsored by the Laboratory Directed Research and Development Program at Oak Ridge National Laboratory (ORNL), which is managed by UT-Battelle, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC05-00OR22725, and used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725. Development of the AutoDock-GPU was supported by the National Institutes of Health (GM069832). We thank Jonathan Lefman and Geetika Gupta (NVIDIA) for essential coordination and communication support.
Sources of information: Directorio de Producción Científica Scopus