Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment.
AuthorsLensink, Marc F.
Chaleil, Raphaël A G
Bates, Paul A
Rodríguez-Lumbreras, Luis Angel
Raghavendra Maddhuri Venkata Subraman, Sai
Moal, Iain H
Ritchie, David W
Chauvot de Beauchêne, Isaure
Echartea, Maria Elisa Ruiz
Barradas Bautista, Didier
Kundrotas, Petras J
Badal, Varsha D
Vakser, Ilya A
Guest, Johnathan D
Pierce, Brian G
Ryan Merideth, Benjamin
Koukos, Panos I
Trellet, Mikael E
Melquiond, Adrien S J
van Noort, Charlotte W
Honorato, Rodrigo V
Bonvin, Alexandre M.J.J.
Wodak, Shoshana J
KAUST DepartmentChemical Science Program
KAUST Catalysis Center (KCC)
Physical Science and Engineering (PSE) Division
Embargo End Date2020-10-16
Permanent link to this recordhttp://hdl.handle.net/10754/658652
MetadataShow full item record
AbstractWe present the results for CAPRI Round 46, the 3rd joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 hetero-complexes. Eight of the homo-oligomer targets and one hetero-dimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homo-dimers, 3 hetero-dimers and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved 'ab-initio' docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the 9 easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance 'gap' was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements. This article is protected by copyright. All rights reserved.
CitationLensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., … Grudinin, S. (2019). Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.25838
SponsorsWe thank the CASP Management and in particular Andriy Kryshtafovych, for valuable help and support in running the assembly prediction challenge. We also express gratitude to the structural biologists who provided the targets for this challenge and to the CAPRI management team and predictor groups for stimulating discussion, valuable input and cooperation.
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