Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment
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We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer 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 homodimers, 3 heterodimers, 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 nine 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.
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The rise of comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine.
“The rise of the comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine [12,13].”
From Challenges in protein docking (2020) · cites this paper as [13]
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- Authors
- Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., Kong, R., Liu, R., Xu, X., 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., Rosell, M., Rodríguez‐Lumbreras, L. A., Romero‐Durana, M., Díaz‐Bueno, L., Fernandez‐Recio, J., Christoffer, C., Terashi, G., Shin, W., Aderinwale, T., Maddhuri Venkata Subraman, S. R., Kihara, D., Kozakov, D., Vajda, S., Porter, K., Padhorny, D., Desta, I., Beglov, D., Ignatov, M., Kotelnikov, S., Moal, I. H., Ritchie, D. W., Chauvot de Beauchêne, I., Maigret, B., Devignes, M., Ruiz Echartea, M. E., 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, P. J., Belkin, S., Chakravarty, D., Badal, V. D., Vakser, I. A., Vreven, T., Vangaveti, S., Borrman, T., Weng, Z., Guest, J. D., Gowthaman, R., Pierce, B. G., Xu, X., Duan, R., Qiu, L., Hou, J., Ryan Merideth, B., Ma, Z., Cheng, J., Zou, X., Koukos, P. I., Roel‐Touris, J., Ambrosetti, F., Geng, C., Schaarschmidt, J., Trellet, M. E., Melquiond, A. S. J., Xue, L., Jiménez‐García, B., van Noort, C. W., Honorato, R. V., Bonvin, A. M. J. J., & Wodak, S. J.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- European Bioinformatics Institute (GB)
- The Francis Crick Institute (GB)
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB) Sorbonne Université Paris France
- Institut polytechnique de Grenoble (FR)
- Jiangsu University of Technology (CN)
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
- Weizmann Institute of Science (IL)
- Faculty of Chemistry University of Gdańsk Gdańsk Poland
- University of Gdańsk (PL)
- Institute of Physics (PL)
- Institute of Computer Science (PL)
- Korea Institute for Advanced Study (KR)
- University of California, Davis (US)
- ETH Zurich (CH)
- Huazhong University of Science and Technology (CN)
- Barcelona Supercomputing Center (ES)
- Barcelona Supercomputing Center (BSC) Barcelona Spain
- Purdue University West Lafayette (US)
- Department of Computer Science Purdue University West Lafayette Indiana
- Stony Brook University (US)
- Department of Biomedical Engineering Boston University Boston Massachusetts
- Boston University (US)
- Moscow Institute of Physics and Technology (RU)
- University of Lorraine, CNRS, Inria, LORIA Nancy France
- King Abdullah University of Science and Technology (SA)
- Parthenope University of Naples (IT)
- Texas A&M University (US)
- Seoul National University (KR)
- Hebrew University of Jerusalem (IL)
- Department of Biological Chemistry, Institute of Live Sciences The Hebrew University of Jerusalem Jerusalem Israel
- Vilnius University (LT)
- University of Kansas (US)
- University of Massachusetts Chan Medical School (US)
- Institute for Bioscience and Biotechnology Research (US)
- University of Missouri (US)
- Dalton Cardiovascular Research Center University of Missouri Columbia Missouri
- Utrecht University (NL)
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
- VIB-VUB Center for Structural Biology (BE)
- Corresponding author
- Lensink, Marc F.
- Wodak, Shoshana J.
- ORCID
- Lensink, Marc F.
- Brysbaert, Guillaume
- Nadzirin, Nurul
- Velankar, Sameer
- Chaleil, Raphaël A. G.
- Bates, Paul A.
- Carbone, Alessandra
- Grudinin, Sergei
- Kong, Ren
- Shi, Hang
- Chang, Shan
- Eisenstein, Miriam
- Czaplewski, Cezary
- Lubecka, Emilia
- Lipska, Agnieszka
- Krupa, Paweł
- Golon, Łukasz
- Samsonov, Sergey
- Liwo, Adam
- Crivelli, Silvia
- Karasikov, Mikhail
- Kadukova, Maria
- Yan, Yumeng
- Huang, Sheng‐You
- Rosell, Mireia
- Rodríguez‐Lumbreras, Luis A.
- Romero‐Durana, Miguel
- Fernandez‐Recio, Juan
- Christoffer, Charles
- Terashi, Genki
- Shin, Woong‐Hee
- Aderinwale, Tunde
- Kihara, Daisuke
- Kozakov, Dima
- Padhorny, Dzmitry
- Desta, Israel
- Ignatov, Mikhail
- Moal, Iain H.
- Ritchie, David W.
- Chauvot de Beauchêne, Isaure
- Maigret, Bernard
- Devignes, Marie‐Dominique
- Barradas‐Bautista, Didier
- Cao, Zhen
- Cavallo, Luigi
- Oliva, Romina
- Cao, Yue
- Shen, Yang
- Baek, Minkyung
- Park, Taeyong
- Woo, Hyeonuk
- Seok, Chaok
- Braitbard, Merav
- Dapkūnas, Justas
- Olechnovič, Kliment
- Venclovas, Česlovas
- Kundrotas, Petras J.
- Belkin, Saveliy
- Chakravarty, Devlina
- Badal, Varsha D.
- Vakser, Ilya A.
- Vreven, Thom
- Vangaveti, Sweta
- Borrman, Tyler
- Weng, Zhiping
- Guest, Johnathan D.
- Gowthaman, Ragul
- Pierce, Brian G.
- Xu, Xianjin
- Duan, Rui
- Qiu, Liming
- Hou, Jie
- Ma, Zhiwei
- Cheng, Jianlin
- Zou, Xiaoqin
- Koukos, Panagiotis I.
- Roel‐Touris, Jorge
- Ambrosetti, Francesco
- Geng, Cunliang
- Schaarschmidt, Jörg
- Trellet, Mikael E.
- Melquiond, Adrien S. J.
- Xue, Li
- Jiménez‐García, Brian
- Honorato, Rodrigo V.
- Bonvin, Alexandre M. J. J.
- Wodak, Shoshana J.
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2019-10-25
- Volume
- 87
- Issue
- 12
- Pages
- 1200-1221
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC7274794
- OpenAlex
- W2980678340
- Cited by
- 122
- References
- 74
- Citations by year
- 2026: 1 · 2025: 15 · 2024: 10 · 2023: 21 · 2022: 16 · 2021: 31 · 2020: 22 · 2019: 5
- FWCI
- 6.09
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship@UMassChan (submittedVersion)
- HAL (submittedVersion, other-oa)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- LillOA (Université de Lille (University Of Lille)) (submittedVersion)
- RIUR (Universidad de La Rioja) (submittedVersion, other-oa)
- King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (submittedVersion)
- CINECA IRIS Institutial research information system (Parthenope University of Naples) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Agence Nationale de la Recherche (ANR‐15‐CE11‐0029‐03)
- Cancer Research UK (FC001003)
- H2020 European Institute of Innovation and Technology (675728, 777536, 823830)
- Lietuvos Mokslo Taryba (S‐MIP‐17‐60)
- Medical Research Council Canada (FC001003)
- National Institutes of Health (R01GM074255, R01GM123055, R35GM124952)
- National Natural Science Foundation of China (31670724)
- National Research Foundation of Korea (2016M3C4A7952630)
- National Science Foundation (DBI1565107)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (718.015.001)
- Wellcome Trust (FC001003)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- homo-oligomers, hetero-oligomers, homodimer, heterodimer, blind prediction, template-based modeling
- MeSH terms
- Algorithms, Binding Sites, Models, Molecular, Protein Binding, Protein Conformation, Proteins, Software, Computational Biology, Protein Interaction Mapping, Databases, Protein, Structural Homology, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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