article Open Access (green) EN 2021-08-28

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Marc F. Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Martyna Maszota‐Zieleniak, Adam K. Sieradzan, Rafał Ślusarz, Patryk A. Wesołowski, Karolina Zięba, Carlos Adriel Del Carpio Munoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo V. Honorato, Zuzana Jandová, Brian Jiménez‐García, Panagiotis I. Koukos, Siri van Keulen, Charlotte W. van Noort, Manon Réau, Jorge Roel‐Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sándor Vajda, Dima Kozakov, Mireia Rosell, Luis Angel Rodríguez‐Lumbreras, Juan Fernández‐Recio, Agnieszka Karczyńska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng‐You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda‐Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak

Proteins Structure Function and Bioinformatics, Vol. 89, Issue 12, pp. 1800–1823 (2021)

Centre National de la Recherche Scientifique, Université de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, European Bioinformatics Institute, Bioinformatics Institute, Wellcome Trust, The Francis Crick Institute, Jiangsu University of Technology, University of Missouri, University of Gdańsk, Gdańsk University of Technology, Gdańsk Medical University, Nagoya City University, Mizuho (Japan), International University Of Health And Welfare Atami Hospital, International University of Health and Welfare, Johns Hopkins University, University of Baltimore, University of Applied Sciences Utrecht, Utrecht University, Innopolis University, Stony Brook University, Boston University, Russian Academy of Sciences, Institute for Computer Aided Design, Barcelona Supercomputing Center, Instituto de Ciencias de la Vid y del Vino, Gobierno de La Rioja, Universitat Politècnica de Catalunya, Institut polytechnique de Grenoble, Centre Inria de l'Université Grenoble Alpes, Laboratoire Jean Kuntzmann, Université Grenoble Alpes, Huazhong University of Science and Technology, Purdue University West Lafayette, Indiana University – Purdue University Indianapolis, Tohoku University, National Institutes for Quantum Science and Technology, Advanced Bioscience Laboratories (United States), Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, King Abdullah University of Science and Technology, Parthenope University of Naples, Texas A&M University at Galveston, Texas A&M University, Seoul National University, Kitasato University, University of Kansas, Vilnius University, VIB-VUB Center for Structural Biology
DOI: 10.1002/prot.26222 PMID: 34453465

Abstract

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Topics

Protein Structure and Dynamics 1.00 Enzyme Structure and Function 0.99 Machine Learning in Materials Science 0.98

Field: Biochemistry, Genetics and Molecular Biology · Subfield: Molecular Biology

Keywords

CASP,Server,Computer science,Template,Protein structure prediction,Data mining,Biology,Computer network,Protein structure

MeSH Terms

Binding SitesBinding SitesBinding SitesBinding SitesBinding SitesModels, MolecularModels, MolecularModels, Molecular

All Available Versions

  • Landing page — Proteins Structure Function and Bioinformatics publishedVersion
  • Landing page — PubMed publishedVersion
  • PDF Landing page — OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) submittedVersion
  • Landing page — PubMed Central submittedVersion
  • Landing page — HAL (Le Centre pour la Communication Scientifique Directe) submittedVersion
  • Landing page — DIGITAL.CSIC (Spanish National Research Council (CSIC)) submittedVersion

Citations by Year

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