MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling

Abstract

Massive sampling in AlphaFold enables access to increased structural diversity. In combination with its efficient confidence ranking, this unlocks elevated modeling capabilities for monomeric structures and foremost for protein assemblies. However, the approach struggles with GPU cost and data storage. Here we introduce MassiveFold, an optimized and customizable version of AlphaFold that runs predictions in parallel, reducing the computing time from several months to hours. MassiveFold is scalable and able to run on anything from a single computer to a large GPU infrastructure, where it can fully benefit from all the computing nodes. Although AlphaFold is very efficient for protein structure prediction, massive sampling is a very GPU demanding task. MassiveFold overcomes this limitation, being capable of parallelizing structure prediction computation.