Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

Ruffolo, J. A.; Chu, L.-S.; Mahajan, S. P.; Gray, J. J.

doi:10.1101/2022.04.20.488972

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bioRxiv · 10.1101/2022.04.20.488972

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

Ruffolo, J. A.·Chu, L.-S.·Mahajan, S. P.·Gray, J. J.

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Abstract

Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances, accurate structural prediction of these loops remains a challenge. Here, we present IgFold, a fast deep learning method for antibody structure prediction. IgFold consists of a pre-trained language model trained on 558M natural antibody sequences followed by graph networks that directly predict backbone atom coordinates. IgFold predicts structures of similar or better quality than alternative methods (including AlphaFold) in significantly less time (under one minute). Accurate structure prediction on this timescale makes possible avenues of investigation that were previously infeasible. As a demonstration of IgFolds capabilities, we predicted structures for 105K paired antibody sequences, expanding the observed antibody structural space by over 40 fold.

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Ruffolo, J. A., Chu, L.-S., Mahajan, S. P., Gray, J. J.. 2022-04-21. Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies. https://doi.org/10.1101/2022.04.20.488972

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