Abstract | ||
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Motivation: In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSAs). The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein-protein interfaces. However, most earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This article introduces a fold-and-dock method based on predicted residue-residue distances with trRosetta. Results: The method can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein-protein docking yielded limited success. However, using alternative methods for generating MSAs allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. This methodology contributed to the best model for one of the CASP14 oligomeric targets, H1065. |
Year | DOI | Venue |
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2022 | 10.1093/bioinformatics/btab760 | BIOINFORMATICS |
DocType | Volume | Issue |
Journal | 38 | 4 |
ISSN | Citations | PageRank |
1367-4803 | 0 | 0.34 |
References | Authors | |
0 | 6 |
Name | Order | Citations | PageRank |
---|---|---|---|
Gabriele Pozzati | 1 | 0 | 0.34 |
Wensi Zhu | 2 | 0 | 0.34 |
Claudio Bassot | 3 | 0 | 0.34 |
John Lamb | 4 | 0 | 1.01 |
Petras Kundrotas | 5 | 0 | 0.34 |
Arne Elofsson | 6 | 0 | 0.34 |