Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.06.22.546069v1?rss=1
Authors: Jeppesen, M., Andre, I.
Abstract:
AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic - tetrahedral, octahedral and icosahedral - symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.
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