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Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment

TitleBlind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment
Publication TypeJournal Article
Year of Publication2019
AuthorsLensink, MF, Brysbaert, G, Nadzirin, N, Velankar, S, Chaleil, RAG, Gerguri, T, Bates, PA, Laine, E, Carbone, A, Grudinin, S, Kong, R, Liu, R-R, Xu, X-M, Shi, H, Chang, S, Eisenstein, M, Karczynska, A, Czaplewski, C, Lubecka, E, Lipska, A, Krupa, P, Mozolewska, M, Golon, Ł, Samsonov, S, Liwo, A, Crivelli, S, Pagès, G, Karasikov, M, Kadukova, M, Yan, Y, Huang, S-Y, Rosell, M, Rodríguez-Lumbreras, LAngel, Romero-Durana, M, Díaz-Bueno, L, Fernandez-Recio, J, Christoffer, C, Terashi, G, Shin, W-H, Aderinwale, T, Subraman, SRaghavendr, Kihara, D, Kozakov, D, Vajda, S, Porter, K, Padhorny, D, Desta, I, Beglov, D, Ignatov, M, Kotelnikov, S, Moal, IH, Ritchie, DW, de Beauchêne, IChauvot, Maigret, B, Devignes, M-D, Echartea, MElisa Ruiz, Barradas-Bautista, D, Cao, Z, Cavallo, L, Oliva, R, Cao, Y, Shen, Y, Baek, M, Park, T, Woo, H, Seok, C, Braitbard, M, Bitton, L, Scheidman-Duhovny, D, DapkŪnas, J, Olechnovič, K, Venclovas, Č, Kundrotas, PJ, Belkin, S, Chakravarty, D, Badal, VD, Vakser, IA, Vreven, T, Vangaveti, S, Borrman, T, Weng, Z, Guest, JD, Gowthaman, R, Pierce, BG, Xu, X, Duan, R, Qiu, L, Hou, J, Merideth, BRyan, Ma, Z, Cheng, J, Zou, X, Koukos, PI, Roel-Touris, J, Ambrosetti, F, Geng, C, Schaarschmidt, J, Trellet, ME, Melquiond, ASJ, Xue, L, Jiménez-García, B, van Noort, CW, Honorato, RV, Bonvin, AMJJ, Wodak, SJ
JournalProteins: Structure, Function, and BioinformaticsProteins: Structure, Function, and BioinformaticsProteins
Issueja
Date Published2019/10/14
ISBN Number0887-3585
Keywordsblind prediction, CAPRI, CASP, docking, oligomeric state, protein assemblies, protein complexes, protein-protein interaction, template-based modeling
Abstract

ABSTRACT We 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.

URLhttps://doi.org/10.1002/prot.25838
Short TitleProteins: Structure, Function, and Bioinformatics