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Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
Zhu, Wensi Shenoy, Aditi Kundrotas, Petras Elofsson, Arne
Zhu, Wensi
Shenoy, Aditi
Kundrotas, Petras
Elofsson, Arne
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Abstract
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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Date
2023-07-05
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Oxford University Press
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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