Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
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Issue Date
2023-07-05Author
Zhu, Wensi
Shenoy, Aditi
Kundrotas, Petras
Elofsson, Arne
Publisher
Oxford University Press
Type
Article
Article Version
Scholarly/refereed, publisher version
Rights
© The Author(s) 2023. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.
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Motivation
Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.Results
We analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g. TM-score) but poorly on another (e.g. DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.Availability and implementation
All scripts, models, and data used to perform the analysis in this study are freely available at https://gitlab.com/ElofssonLab/afm-benchmark.
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Citation
Wensi Zhu and others, Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes, Bioinformatics, Volume 39, Issue 7, July 2023, btad424, https://doi.org/10.1093/bioinformatics/btad424
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