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 language | English |
---|---|
Title of host publication | PEARC 2022 Conference Series - Practice and Experience in Advanced Research Computing 2022 - Revolutionary |
Subtitle of host publication | Computing, Connections, You |
Publisher | Association for Computing Machinery, Inc |
ISBN (Electronic) | 9781450391610 |
DOIs | |
State | Published - Jul 8 2022 |
Externally published | Yes |
Event | 2022 Conference on Practice and Experience in Advanced Research Computing: Revolutionary: Computing, Connections, You, PEARC 2022 - Boston, United States Duration: Jul 10 2022 → Jul 14 2022 |
Publication series
Name | PEARC 2022 Conference Series - Practice and Experience in Advanced Research Computing 2022 - Revolutionary: Computing, Connections, You |
---|
Conference
Conference | 2022 Conference on Practice and Experience in Advanced Research Computing: Revolutionary: Computing, Connections, You, PEARC 2022 |
---|---|
Country/Territory | United States |
City | Boston |
Period | 07/10/22 → 07/14/22 |
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