Enabling Large-Scale and Ultra-Large AlphaFold3 Predictions with Distributed High-Throughput Computing

CHTC facilitator Danny Morales explains how his team solved AlphaFold3’s core HTC challenge: routing jobs to nodes where the 750 GB reference database is already staged, rather than transferring it per job. By treating data as a schedulable resource via HTCondor ClassAds and caching alignments for reuse, they cut preprocessing by ~89% and enabled protein-protein interaction screenings at a scale previously impossible on distributed systems.