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

Journal article

M. Lensink, G. Brysbaert, Théo Mauri, Nurul Nadzirin, S. Velankar, Raphael A. G. Chaleil, Tereza Clarence, P. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Rajashree Roy, Farhan Quadir, Jian Liu, Jian-Lin Cheng, Anna Antoniak, C. Czaplewski, A. Giełdoń, Mateusz Kogut, A. Lipska, A. Liwo, E. Lubecka, M. Maszota-Zieleniak, A. Sieradzan, R. Ślusarz, P. Wesołowski, Karolina Zieba, C. A. Del Carpio Munoz, E. Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, A. Bonvin, Francesco Ambrosetti, R. Honorato, Z. Jandova, Brian Jiménez-García, Panagiotis I. Koukos, S. V. van Keulen, Charlotte van Noort, M. Réau, Jorge Roel‐Touris, S. Kotelnikov, D. Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel T. Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, S. Vajda, D. Kozakov, Mireia Rosell, L. A. Rodríguez-Lumbreras, J. Fernández-Recio, Agnieszka S. Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles W Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, D. Kihara, Tsukasa Nakamura, Y. Hanazono, R. Gowthaman, Johnathan D. Guest, Rui Yin, G. Taherzadeh, B. Pierce, Didier Barradas-Bautista, Zhen Cao, L. Cavallo, R. Oliva, Yuan-Fei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, S. Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, P. Kundrotas, Amar Singh, I. Vakser, J. Dapkūnas, K. Olechnovič, Č. Venclovas, R. Duan, Liming Qiu, Shuang Zhang, Xiaoqin Zou, S. Wodak
Proteins: Structure, Function, and Bioinformatics, 2021

Semantic Scholar DOI PubMedCentral PubMed

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APA Click to copy
Lensink, M., Brysbaert, G., Mauri, T., Nadzirin, N., Velankar, S., Chaleil, R. A. G., … Wodak, S. (2021). Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics.

Chicago/Turabian Click to copy
Lensink, M., G. Brysbaert, Théo Mauri, Nurul Nadzirin, S. Velankar, Raphael A. G. Chaleil, Tereza Clarence, et al. “Prediction of Protein Assemblies, the next Frontier: The CASP14-CAPRI Experiment.” Proteins: Structure, Function, and Bioinformatics (2021).

MLA Click to copy
Lensink, M., et al. “Prediction of Protein Assemblies, the next Frontier: The CASP14-CAPRI Experiment.” Proteins: Structure, Function, and Bioinformatics, 2021.

BibTeX Click to copy

@article{m2021a,
  title = {Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment},
  year = {2021},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  author = {Lensink, M. and Brysbaert, G. and Mauri, Théo and Nadzirin, Nurul and Velankar, S. and Chaleil, Raphael A. G. and Clarence, Tereza and Bates, P. and Kong, Ren and Liu, Bin and Yang, Guangbo and Liu, Ming and Shi, Hang and Lu, Xufeng and Chang, Shan and Roy, Rajashree and Quadir, Farhan and Liu, Jian and Cheng, Jian-Lin and Antoniak, Anna and Czaplewski, C. and Giełdoń, A. and Kogut, Mateusz and Lipska, A. and Liwo, A. and Lubecka, E. and Maszota-Zieleniak, M. and Sieradzan, A. and Ślusarz, R. and Wesołowski, P. and Zieba, Karolina and Munoz, C. A. Del Carpio and Ichiishi, E. and Harmalkar, Ameya and Gray, Jeffrey J. and Bonvin, A. and Ambrosetti, Francesco and Honorato, R. and Jandova, Z. and Jiménez-García, Brian and Koukos, Panagiotis I. and van Keulen, S. V. and van Noort, Charlotte and Réau, M. and Roel‐Touris, Jorge and Kotelnikov, S. and Padhorny, D. and Porter, Kathryn A. and Alekseenko, Andrey and Ignatov, Mikhail and Desta, Israel T. and Ashizawa, Ryota and Sun, Zhuyezi and Ghani, Usman and Hashemi, Nasser and Vajda, S. and Kozakov, D. and Rosell, Mireia and Rodríguez-Lumbreras, L. A. and Fernández-Recio, J. and Karczynska, Agnieszka S. and Grudinin, Sergei and Yan, Yumeng and Li, Hao and Lin, Peicong and Huang, Sheng-You and Christoffer, Charles W and Terashi, Genki and Verburgt, Jacob and Sarkar, Daipayan and Aderinwale, Tunde and Wang, Xiao and Kihara, D. and Nakamura, Tsukasa and Hanazono, Y. and Gowthaman, R. and Guest, Johnathan D. and Yin, Rui and Taherzadeh, G. and Pierce, B. and Barradas-Bautista, Didier and Cao, Zhen and Cavallo, L. and Oliva, R. and Sun, Yuan-Fei and Zhu, Shaowen and Shen, Yang and Park, Taeyong and Woo, Hyeonuk and Yang, Jinsol and Kwon, Sohee and Won, Jonghun and Seok, Chaok and Kiyota, Yasuomi and Kobayashi, S. and Harada, Yoshiki and Takeda-Shitaka, Mayuko and Kundrotas, P. and Singh, Amar and Vakser, I. and Dapkūnas, J. and Olechnovič, K. and Venclovas, Č. and Duan, R. and Qiu, Liming and Zhang, Shuang and Zou, Xiaoqin and Wodak, S.}
}

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.