Supercomputing pipelines search for therapeutics against covid-19

Josh Vincent Vermaas, Ada Sedova, Matthew B. Baker, Swen Boehm, David M. Rogers, Jeff Larkin, Jens Glaser, Micholas D. Smith, Oscar Hernandez, Jeremy C. Smith

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

The urgent search for drugs to combat SARS-CoV-2 has included the use of supercomputers. The use of general-purpose graphical processing units (GPUs), massive parallelism, and new software for high-performance computing (HPC) has allowed researchers to search the vast chemical space of potential drugs faster than ever before. We developed a new drug discovery pipeline using the Summit supercomputer at Oak Ridge National Laboratory to help pioneer this effort, with new platforms that incorporate GPU-accelerated simulation and allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins. This effort will accelerate the process of developing drugs to combat the current COVID-19 pandemic and other diseases.

Original languageEnglish
Article number9250525
Pages (from-to)7-16
Number of pages10
JournalComputing in Science and Engineering
Volume23
Issue number1
DOIs
StatePublished - Jan 1 2021

Funding

This work was supported by the Laboratory Directed Research and Development Program The authors would like to thank Scott Le Grand (NVI-DIA), Aaron Scheinberg (Jubilee Development), and Andreas Tillack (Scripps Research) along with the rest of the NVIDIA and Scripps teams for their work on AutoDock-GPU on Summit and advice and support. We also acknowledge the contributions Rupesh Agarwal and Mathialakan Thavappiragasam for their input and expertise in the early stages of pipeline development. This work was supported by the Laboratory Directed Research and Development Program at Oak Ridge National Laboratory, which is managed by UT-Battelle, LLC, for the U.S. Department of Energy (DOE) under Contract DE-AC05-00OR22725. This work also used resources, services, and support provided via the COVID-19 HPC Consortium (https://covid19-hpc-consortium.org/), which is a unique private–public effort to bring together government, industry, and academic leaders who are volunteering free compute time and resources in support of COVID-19 research, and used resources of the Oak Ridge Leadership Computing Facility at the ORNL.

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