MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling
Nessim Raouraoua, Claudio Mirabello, Thibaut Véry, Christophe Blanchet, Björn Wallner, Marc F. Lensink, Guillaume Brysbaert
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.