ArticleProteins2019
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
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Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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69citing papers in PubMed
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69 citing papers in PubMed.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- Accurate protein-protein interactions modeling through physics-informed geometric invariant learning.Communications biology · 2026Article
- COCOMAPS 2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes.Bioinformatics (Oxford, England) · 2025Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.Nature communications · 2025Article
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- 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
- Evaluation of Angiotensin-Converting Enzyme 2 ExpressionACS pharmacology & translational science · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.Proteins · 2023Article
- Article
- The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15.Proteins · 2023Article
- Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15.Communications biology · 2023Article
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
- Assessment of three-dimensional RNA structure prediction in CASP15.bioRxiv : the preprint server for biology · 2023Article
- The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15.bioRxiv : the preprint server for biology · 2023Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
105 authors.
Marc F LensinkUniversity of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.ORCID 0000-0003-3957-9470
Guillaume BrysbaertUniversity of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
Nurul NadzirinEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Sameer VelankarEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Raphaël A G ChaleilBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.ORCID 0000-0003-2759-2088
Tereza GerguriBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
Paul A BatesBiomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.ORCID 0000-0003-0621-0925
Elodie LaineCNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.
Alessandra CarboneCNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.ORCID 0000-0003-2098-5743
Sergei GrudininUniversité Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.
Ren KongInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Ran-Ran LiuInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Xi-Ming XuInstitute 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.
Shan ChangInstitute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.ORCID 0000-0001-7169-9398
Miriam EisensteinDepartment of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Agnieszka KarczynskaFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
Cezary CzaplewskiFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.ORCID 0000-0002-0294-3403
Emilia LubeckaInstitute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland.
Agnieszka LipskaFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
Paweł KrupaPolish Academy of Sciences, Institute of Physics, Warsaw, Poland.
Magdalena MozolewskaPolish Academy of Sciences, Institute of Computer Science, Warsaw, Poland.
Łukasz GolonFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
Sergey SamsonovFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
Adam LiwoFaculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
Silvia CrivelliDepartment of Computer Science, UC Davis, Davis, California.
Guillaume PagèsUniversité Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.
Mikhail KarasikovDepartment of Computer Science, ETH, Zurich, Switzerland.
Maria KadukovaUniversité Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.
Yumeng YanSchool of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
Sheng-You HuangSchool of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.ORCID 0000-0002-4209-4565
Mireia RosellBarcelona Supercomputing Center (BSC), Barcelona, Spain.ORCID 0000-0002-7787-8896
Luis A Rodríguez-LumbrerasBarcelona Supercomputing Center (BSC), Barcelona, Spain.
Miguel Romero-DuranaBarcelona Supercomputing Center (BSC), Barcelona, Spain.
Lucía Díaz-BuenoBarcelona Supercomputing Center (BSC), Barcelona, Spain.
Juan Fernandez-RecioBarcelona Supercomputing Center (BSC), Barcelona, Spain.ORCID 0000-0002-3986-7686
Charles ChristofferDepartment of Computer Science, Purdue University, West Lafayette, Indiana.ORCID 0000-0002-6163-6323
Genki TerashiDepartment of Biological Sciences, Purdue University, West Lafayette, Indiana.
Woong-Hee ShinDepartment of Biological Sciences, Purdue University, West Lafayette, Indiana.
Tunde AderinwaleDepartment of Computer Science, Purdue University, West Lafayette, Indiana.
Sai Raghavendra Maddhuri Venkata SubramanDepartment of Computer Science, Purdue University, West Lafayette, Indiana.
Daisuke KiharaDepartment of Computer Science, Purdue University, West Lafayette, Indiana.ORCID 0000-0003-4091-6614
Dima KozakovLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.ORCID 0000-0003-0464-4500
Sandor VajdaDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts.
Kathryn PorterDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts.
Dzmitry PadhornyLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.
Israel DestaDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts.
Dmitri BeglovDepartment of Biomedical Engineering, Boston University, Boston, Massachusetts.
Mikhail IgnatovLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.
Sergey KotelnikovMoscow Institute of Physics and Technology, Dolgoprudniy, Russia.
Iain H MoalEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-4960-5487
David W RitchieUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, France.
Isaure Chauvot de BeauchêneUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, France.ORCID 0000-0002-7035-3042
Bernard MaigretUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, France.
Marie-Dominique DevignesUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, France.
Maria E Ruiz EcharteaUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, France.
Didier Barradas-BautistaPhysical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Zhen CaoPhysical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Luigi CavalloPhysical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Romina OlivaDepartment of Sciences and Technologies, University of Naples "Parthenope", Napoli, Italy.
Yue CaoDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, Texas.
Yang ShenDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, Texas.ORCID 0000-0002-1703-7796
Minkyung BaekDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Taeyong ParkDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Hyeonuk WooDepartment 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
Merav BraitbardDepartment of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
Lirane BittonSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
Dina Scheidman-DuhovnyDepartment of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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
Petras J KundrotasComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
Saveliy BelkinComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
Devlina ChakravartyComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
Varsha D BadalComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
Ilya A VakserComputational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.ORCID 0000-0002-5743-2934
Thom VrevenBioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.ORCID 0000-0003-3413-806X
Sweta VangavetiBioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Tyler BorrmanBioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Zhiping WengBioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.ORCID 0000-0002-3032-7966
Johnathan D GuestUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.
Ragul GowthamanUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.
Brian G PierceUniversity of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.
Xianjin XuDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Rui DuanDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Liming QiuDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Jie HouDepartment of Computer Science, University of Missouri, Columbia, Missouri.
Benjamin Ryan MeridethDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Zhiwei MaDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Jianlin ChengDepartment of Computer Science, University of Missouri, Columbia, Missouri.
Xiaoqin ZouDalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
Panagiotis I KoukosComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Jorge Roel-TourisComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Francesco AmbrosettiComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Cunliang GengComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.ORCID 0000-0002-1409-8358
Jörg SchaarschmidtComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Mikael E TrelletComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Adrien S J MelquiondComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Li XueComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Brian Jiménez-GarcíaComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Charlotte W van NoortComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Rodrigo V HonoratoComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
Alexandre M J J BonvinComputational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.ORCID 0000-0001-7369-1322
Shoshana J WodakVIB Structural Biology Research Center, VUB, Brussels, Belgium.ORCID 0000-0002-0701-6545
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
$6.2MIntegrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8MUnraveling molecular and system-level mechanisms of human disease-associated protein mutationsR35GM124952 · NIGMS · TEXAS ENGINEERING EXPERIMENT STATION · PI Yang Shen · 2017 to 2026
$2.9MDatabase and software development for protein-nucleic acid structure predicationR01GM109980 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI ZOU, XIAOQIN · 2015 to 2019
$1.5MGraduate Training in VirologyT32AI125186 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI SIMON, ANNE ELIZABETH · 2016 to 2020
$1.3MStructural Modeling of Multifarious Protein ComplexesR01GM123055 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2017 to 2020
$1.2MFast energy evaluation for multi-protein systemsR21GM127952 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI KOZAKOV, DMYTRO · 2018 to 2019
$432kCancer Research UK 10748Cancer Research UK FC001003Medical Research Council FC001003NIAID NIH HHS T32 AI125186NIGMS NIH HHS R01 GM074255NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM109980NIGMS NIH HHS R01 GM123055NIGMS NIH HHS R21 GM127952NIGMS NIH HHS R35 GM118078NIGMS NIH HHS R35 GM124952NIH HHS R01GM074255NIH HHS R01GM123055NIH HHS R35GM124952Wellcome Trust FC001003
Abstract
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.
Indexed as
Computational BiologyProtein ConformationSoftwareAlgorithmsBinding SitesDatabases, ProteinModels, MolecularProtein BindingProtein Interaction MappingProteinsStructural Homology, ProteinProteinsblind predictionCAPRICASPdockingoligomeric stateprotein assembliesprotein complexesprotein-protein interactiontemplate-based modeling
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