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Improved prediction of protein-protein interactions using AlphaFold2

View ORCID ProfileP. Bryant, View ORCID ProfileG. Pozzati, View ORCID ProfileA. Elofsson
doi: https://doi.org/10.1101/2021.09.15.460468
P. Bryant
1Science for Life Laboratory, 172 21 Solna, Sweden
2Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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  • For correspondence: patrick.bryant@scilifelab.se
G. Pozzati
1Science for Life Laboratory, 172 21 Solna, Sweden
2Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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A. Elofsson
1Science for Life Laboratory, 172 21 Solna, Sweden
2Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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Abstract

Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimized multiple sequence alignments, generate models with acceptable quality (DockQ≥0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR. The protocol can be found at: https://gitlab.com/ElofssonLab/FoldDock.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • After reviews we have updated the manuscript. In short two major things have changed 1) We have introduced a pDockQ score that predicts the DockQ score for each protein-protein interactions. This improves both separation of good and bad models and interacting and non-interacting proteins. 2) We have added comparisons to (a) state of the art docking method and (b) alphafold-multimer.

  • https://gitlab.com/ElofssonLab/FoldDock.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 15, 2021.
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Improved prediction of protein-protein interactions using AlphaFold2
P. Bryant, G. Pozzati, A. Elofsson
bioRxiv 2021.09.15.460468; doi: https://doi.org/10.1101/2021.09.15.460468
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Improved prediction of protein-protein interactions using AlphaFold2
P. Bryant, G. Pozzati, A. Elofsson
bioRxiv 2021.09.15.460468; doi: https://doi.org/10.1101/2021.09.15.460468

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