AlphaFold2 Workflow Optimization for High Throughput Predictions in HPC Environment

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.