AlphaFold2 Workflow Optimization for High Throughput Predictions in HPC Environment

Edwin Fernando Posada, Francisco McGee, Richard Berger, Mitchell Dorrell, Jason Lamanna, Sergiu Sanielevici, Vincenzo Carnevale

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

In this work, we propose a high-throughput implementation that executes AlphaFold2 efficiently in a High-Performance Computing environment. In this case, we have tested our proposed workflow with the T1050 CASP14 sequence on PSC's Bridges-2 HPC system. The results showed an improvement in computation-only runtimes and the opportunity to reuse the protein databases when calculating many structures simultaneously, which would lead to massive time savings while maximizing the utilization of computing resources.

Original languageEnglish
Title of host publicationPEARC 2022 Conference Series - Practice and Experience in Advanced Research Computing 2022 - Revolutionary
Subtitle of host publicationComputing, Connections, You
PublisherAssociation for Computing Machinery, Inc
ISBN (Electronic)9781450391610
DOIs
StatePublished - Jul 8 2022
Externally publishedYes
Event2022 Conference on Practice and Experience in Advanced Research Computing: Revolutionary: Computing, Connections, You, PEARC 2022 - Boston, United States
Duration: Jul 10 2022Jul 14 2022

Publication series

NamePEARC 2022 Conference Series - Practice and Experience in Advanced Research Computing 2022 - Revolutionary: Computing, Connections, You

Conference

Conference2022 Conference on Practice and Experience in Advanced Research Computing: Revolutionary: Computing, Connections, You, PEARC 2022
Country/TerritoryUnited States
CityBoston
Period07/10/2207/14/22

Funding

This work was funded in part by the National Institutes of Health (R01GM093290, S10OD020095, and R01GM131048; V.C.), and the National Science Foundation through Grant no. IOS-1934848 (V.C.). This research includes calculations carried out on HPC resources supported in part by the National Science Foundation through major research instrumentation grant number 1625061 and through the Extreme Science and Engineering Discovery Environment (XSEDE), grant number ACI-1548562; as well as by the US Army Research Laboratory under contract number W911NF-16-2-0189.

Keywords

  • AlphaFold2
  • High-Performance Computing
  • Software Optimization
  • bioinformatics

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