Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Autor:	Lensink MF; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Brysbaert G; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Nadzirin N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Chaleil RAG; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Gerguri T; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Bates PA; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Laine E; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France., Carbone A; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.; Institut Universitaire de France (IUF), Paris, France., Grudinin S; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Kong R; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Liu RR; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Xu XM; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Shi H; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Chang S; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Eisenstein M; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel., Karczynska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Lubecka E; Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland., Lipska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Krupa P; Polish Academy of Sciences, Institute of Physics, Warsaw, Poland., Mozolewska M; Polish Academy of Sciences, Institute of Computer Science, Warsaw, Poland., Golon Ł; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Samsonov S; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea., Crivelli S; Department of Computer Science, UC Davis, Davis, California., Pagès G; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Karasikov M; Department of Computer Science, ETH, Zurich, Switzerland., Kadukova M; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia., Yan Y; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Huang SY; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Rosell M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Rodríguez-Lumbreras LA; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Romero-Durana M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Díaz-Bueno L; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Fernandez-Recio J; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain.; Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain., Christoffer C; Department of Computer Science, Purdue University, West Lafayette, Indiana., Terashi G; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Shin WH; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Aderinwale T; Department of Computer Science, Purdue University, West Lafayette, Indiana., Maddhuri Venkata Subraman SR; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kihara D; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kozakov D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Vajda S; Department of Biomedical Engineering, Boston University, Boston, Massachusetts.; Department of Chemistry, Boston University, Boston, Massachusetts., Porter K; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Padhorny D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Desta I; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Beglov D; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Ignatov M; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Kotelnikov S; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Moal IH; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Ritchie DW; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Chauvot de Beauchêne I; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Maigret B; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Devignes MD; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Ruiz Echartea ME; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Barradas-Bautista D; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cao Z; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cavallo L; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Oliva R; Department of Sciences and Technologies, University of Naples 'Parthenope', Napoli, Italy., Cao Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Baek M; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Park T; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Woo H; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Seok C; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Braitbard M; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel., Bitton L; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Scheidman-Duhovny D; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Dapkūnas J; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Olechnovič K; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Venclovas Č; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Kundrotas PJ; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Belkin S; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Chakravarty D; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Badal VD; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vakser IA; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vreven T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Vangaveti S; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Borrman T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Weng Z; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Guest JD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Xu X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Duan R; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Qiu L; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Hou J; Department of Computer Science, University of Missouri, Columbia, Missouri., Ryan Merideth B; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Ma Z; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri., Cheng J; Department of Computer Science, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Zou X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.; Department of Biochemistry, University of Missouri, Columbia, Missouri., Koukos PI; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Roel-Touris J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Ambrosetti F; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Geng C; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Schaarschmidt J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Trellet ME; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Melquiond ASJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Xue L; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jiménez-García B; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., van Noort CW; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Honorato RV; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Bonvin AMJJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Wodak SJ; VIB Structural Biology Research Center, VUB, Brussels, Belgium.
Jazyk:	angličtina
Zdroj:	Proteins [Proteins] 2019 Dec; Vol. 87 (12), pp. 1200-1221. Date of Electronic Publication: 2019 Oct 25.
DOI:	10.1002/prot.25838
Abstrakt:	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. (© 2019 Wiley Periodicals, Inc.)
Databáze:	MEDLINE
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