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Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic resolution in some cases, and with accelerators like GPUs and TPUs making inference using large models rapid, fast genome-level structure prediction becomes an obvious aim. Leadership-class computing resources can be used to perform genome-scale protein structure prediction using state-of-the-art deep learning models, providing a wealth of new data for systems biology applications. Here we describe our efforts to efficiently deploy the AlphaFold2 program, for full-proteome structure prediction, at scale on the Oak Ridge Leadership Computing Facility's resources, including the Summit supercomputer. We performed inference to produce the predicted structures for 35,634 protein sequences, corresponding to three prokaryotic proteomes and one plant proteome, using under 4,000 total Summit node hours, equivalent to using the majority of the supercomputer for one hour. We also designed an optimized structure refinement that reduced the time for the relaxation stage of the AlphaFold pipeline by over 10X for longer sequences. We demonstrate the types of analyses that can be performed on proteome-scale collections of sequences, including a search for novel quaternary structures and implications for functional annotation.