ArticleProteins2021
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
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Article in Proteins, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65citing papers in PubMed
7.8field-weighted citation impact, top 2% of its field
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65 citing papers in PubMed, 125 citations in OpenAlex.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- Biomolecular Interaction Prediction in the Pre- and Post-AlphaFold Era: The 8th CAPRI Evaluation.Proteins · 2026Article
- Massive Sampling Strategy for Antibody-Antigen Targets in CAPRI Round 55 With MassiveFold.Proteins · 2026Article
- Performance of pyDock in 8th CAPRI: Energy-Based Scoring Applied to Docking and AlphaFold Models.Proteins · 2026Article
- Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.Proteins · 2026Article
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- Accurate protein-protein interactions modeling through physics-informed geometric invariant learning.Communications biology · 2026Article
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
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- High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.Nature communications · 2025Article
- Boosting AlphaFold protein tertiary structure prediction through MSA engineering and extensive model sampling and ranking in CASP16.Communications biology · 2025Article
- Increasing the fraction of correct solutions in ensembles of protein-protein docking models by an iterative consensus algorithm.Protein science : a publication of the Protein Society · 2025Article
- AlphaFold model quality self-assessment improvement via deep graph learning.Protein science : a publication of the Protein Society · 2025Article
- GRAMMCell: Docking-based Cell Modeling Resource.Journal of molecular biology · 2025Article
- Article
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
- Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.The journal of physical chemistry. B · 2025Article
- Decoding Solubility Signatures from Amyloid Monomer Energy Landscapes.Journal of chemical theory and computation · 2025Article
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- Recent advances and challenges in protein complex model accuracy estimation.Computational and structural biotechnology journal · 2024Review
5 more citing papers are in PubMed but not listed here.
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Authors and funding
109 authors at 20 institutions in 14 countries.
Marc F LensinkCNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.ORCID 0000-0003-3957-9470
Guillaume BrysbaertCNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Théo MauriCNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Nurul NadzirinProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
Sameer VelankarProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
Raphael A G ChaleilBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.ORCID 0000-0003-2759-2088
Tereza ClarenceBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
Paul A BatesBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.ORCID 0000-0003-0621-0925
Ren KongInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Bin LiuInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Guangbo YangInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Ming LiuInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Hang ShiInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Xufeng LuInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Shan ChangInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.ORCID 0000-0001-7169-9398
Raj S RoyDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
Farhan QuadirDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
Jian LiuDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
Jianlin ChengDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
Anna AntoniakFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Cezary CzaplewskiFaculty of Chemistry, University of Gdansk, Gdansk, Poland.ORCID 0000-0002-0294-3403
Artur GiełdońFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Mateusz KogutFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Agnieszka G LipskaFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Adam LiwoFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Emilia A LubeckaFaculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland.
Martyna Maszota-ZieleniakFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Adam K SieradzanFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Rafał ŚlusarzFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Patryk A WesołowskiFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Karolina ZiębaFaculty of Chemistry, University of Gdansk, Gdansk, Poland.
Carlos A Del Carpio MuñozGraduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.
Eiichiro IchiishiInternational University of Health and Welfare Hospital (IUHW Hospital), Nasushiobara City, Japan.
Ameya HarmalkarChemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
Jeffrey J GrayChemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
Alexandre M J J BonvinComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.ORCID 0000-0001-7369-1322
Francesco AmbrosettiComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Rodrigo Vargas HonoratoComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Zuzana JandovaComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Brian Jiménez-GarcíaComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Panagiotis I KoukosComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Siri Van KeulenComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Charlotte W Van NoortComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Manon RéauComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Jorge Roel-TourisComputational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Sergei KotelnikovDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
Dzmitry PadhornyDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.ORCID 0000-0002-7840-8677
Kathryn A PorterDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
Andrey AlekseenkoDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
Mikhail IgnatovDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
Israel DestaDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
Ryota AshizawaDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
Zhuyezi SunDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
Usman GhaniDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
Nasser HashemiDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
Sandor VajdaDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.ORCID 0000-0003-1540-8220
Dima KozakovDepartment of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.ORCID 0000-0003-0464-4500
Mireia RosellInstituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.
Luis A Rodríguez-LumbrerasInstituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.
Juan Fernandez-RecioInstituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.ORCID 0000-0002-3986-7686
Agnieszka KarczynskaUniversité Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France.
Sergei GrudininUniversité Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France.ORCID 0000-0002-1903-7220
Yumeng YanSchool of Physics, Huazhong University of Science and Technology, Wuhan, China.
Hao LiSchool of Physics, Huazhong University of Science and Technology, Wuhan, China.
Peicong LinSchool of Physics, Huazhong University of Science and Technology, Wuhan, China.
Sheng-You HuangSchool of Physics, Huazhong University of Science and Technology, Wuhan, China.ORCID 0000-0002-4209-4565
Charles ChristofferDepartment of Computer Science, Purdue University, West Lafayette, Indiana, USA.ORCID 0000-0002-6163-6323
Genki TerashiDepartment of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
Jacob VerburgtDepartment of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
Daipayan SarkarDepartment of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
Tunde AderinwaleDepartment of Computer Science, Purdue University, West Lafayette, Indiana, USA.
Xiao WangDepartment of Computer Science, Purdue University, West Lafayette, Indiana, USA.
Daisuke KiharaDepartment of Computer Science, Purdue University, West Lafayette, Indiana, USA.ORCID 0000-0003-4091-6614
Tsukasa NakamuraGraduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.
Yuya HanazonoInstitute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, Japan.
Ragul GowthamanUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.
Johnathan D GuestUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.
Rui YinUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.
Ghazaleh TaherzadehUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.
Brian G PierceUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.
Didier Barradas-BautistaKing Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Zhen CaoKing Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Luigi CavalloKing Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Romina OlivaUniversity of Naples "Parthenope", Napoli, Italy.
Yuanfei SunDepartment of Electrical and Computer Engineering, Texas A&M University, Texas, USA.
Shaowen ZhuDepartment of Electrical and Computer Engineering, Texas A&M University, Texas, USA.
Yang ShenDepartment of Electrical and Computer Engineering, Texas A&M University, Texas, USA.ORCID 0000-0002-1703-7796
Taeyong ParkDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Hyeonuk WooDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Jinsol YangDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Sohee KwonDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Jonghun WonDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Chaok SeokDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.ORCID 0000-0002-1419-9888
Yasuomi KiyotaSchool of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan.
Shinpei KobayashiSchool of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan.
Yoshiki HaradaSchool of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan.
Mayuko Takeda-ShitakaSchool of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan.
Petras J KundrotasComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.
Amar SinghComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.
Ilya A VakserComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.ORCID 0000-0002-5743-2934
Justas DapkūnasInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-0496-6107
Kliment OlechnovičInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Česlovas VenclovasInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-4215-0213
Rui DuanDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.
Liming QiuDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.
Xianjin XuDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.
Shuang ZhangDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.
Xiaoqin ZouInstitute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA.ORCID 0000-0003-0637-8648
Shoshana J WodakCenter for Structural Biology, VIB-VUB, Brussels, Belgium.ORCID 0000-0002-0701-6545
University of Gdańsk · PLUniversity of Applied Sciences Utrecht · NLUniversity of Missouri · USJiangsu University of Technology · CNPurdue University West Lafayette · USBoston University · USSeoul National University · KRAdvanced Bioscience Laboratories (United States) · USHuazhong University of Science and Technology · CNKitasato University · JPStony Brook University · USBarcelona Supercomputing Center · ESCentre National de la Recherche Scientifique · FRKing Abdullah University of Science and Technology · SATexas A&M University at Galveston · USThe Francis Crick Institute · GBUniversity of Kansas · USVilnius University · LTEuropean Bioinformatics Institute · GBInstitut polytechnique de Grenoble · FR
Funding
Analysis and Prediction of Molecular InteractionsR35GM118078 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI SANDOR VAJDA · 2016 to 2026
$6.5MIntegrated Resource for Protein Recognition StudiesR01GM074255 · NIGMS · UNIVERSITY OF KANSAS LAWRENCE · PI VAKSER, ILYA · 2005 to 2024
$6.2MSolvation modeling for next-gen biomolecule simulationsRM1GM135136 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI COUTSIAS, EVANGELOS A., DILL, KEN A · 2020 to 2024
$6.0MPrediction of the Structure of Therapeutic Antibodies with their AntigensR01GM078221 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GRAY, JEFFREY J · 2006 to 2020
$4.0MIntegrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8MStructure prediction and in silico screening of protein-peptide interactionsR35GM136409 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI XIAOQIN ZOU · 2020 to 2026
$2.9MMechanism of BK Channel GatingR01HL142301 · NHLBI · WASHINGTON UNIVERSITY · PI SILVA, JONATHAN R · 2018 to 2021
$2.9MUnraveling molecular and system-level mechanisms of human disease-associated protein mutationsR35GM124952 · NIGMS · TEXAS ENGINEERING EXPERIMENT STATION · PI Yang Shen · 2017 to 2026
$2.9MPurdue University Molecular Biophysics Training ProgramT32GM132024 · NIGMS · PURDUE UNIVERSITY · PI Angeline Marie Lyon, John Tesmer · 2019 to 2026
$2.0MBuilding protein structure models for intermediate resolution cryo-electron microscopy mapsR01GM133840 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2020 to 2023
$1.6MDatabase and software development for protein-nucleic acid structure predicationR01GM109980 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI ZOU, XIAOQIN · 2015 to 2019
$1.5MStructural Modeling of Multifarious Protein ComplexesR01GM123055 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2017 to 2020
$1.2MCancer Research UK 10748Cancer Research UK FC001003Medical Research CouncilNHLBI NIH HHS R01 HL142301NIGMS NIH HHS R01 GM074255NIGMS NIH HHS R01 GM078221NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM109980NIGMS NIH HHS R01 GM123055NIGMS NIH HHS R01 GM133840NIGMS NIH HHS R21 GM127952NIGMS NIH HHS R35 GM118078NIGMS NIH HHS R35 GM124952NIGMS NIH HHS R35 GM136409NIGMS NIH HHS RM1 GM135136NIGMS NIH HHS T32 GM132024Wellcome Trust
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.
Indexed as
Models, MolecularProteinsSoftwareBinding SitesComputational BiologyMolecular Docking SimulationProtein Interaction Domains and MotifsSequence Analysis, ProteinProteinsblind predictionCAPRICASPdockingoligomeric stateprotein assembliesprotein complexesprotein dockingprotein-protein interactiontemplate-based modeling
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