Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Marc F Lensink; Sameer Velankar; Andriy Kryshtafovych; Shen-You Huang; Dina Schneidman-Duhovny; Andrej Sali; Joan Segura; Narcis Fernandez-Fuentes; Shruthi Viswanath; Ron Elber; Sergei Grudinin; Petr Popov; Emilie Neveu; Hasup Lee; Minkyung Baek; Sangwoo Park; Lim Heo; Gyu Rie Lee; Chaok Seok; Sanbo Qin; Huan-Xiang Zhou; David W Ritchie; Bernard Maigret; Marie-Dominique Devignes; Anisah Ghoorah; Mieczyslaw Torchala; Raphaël A G Chaleil; Paul A Bates; Efrat Ben-Zeev; Miriam Eisenstein; Surendra S Negi; Zhiping Weng; Thom Vreven; Brian G Pierce; Tyler M Borrman; Jinchao Yu; Françoise Ochsenbein; Raphaël Guerois; Anna Vangone; João P G L M Rodrigues; Gydo van Zundert; Mehdi Nellen; Li Xue; Ezgi Karaca; Adrien S J Melquiond; Koen Visscher; Panagiotis L Kastritis; Alexandre M J J Bonvin; Xianjin Xu; Liming Qiu; Chengfei Yan; Jilong Li; Zhiwei Ma; Jianlin Cheng; Xiaoqin Zou; Yang Shen; Lenna X Peterson; Hyung-Rae Kim; Amit Roy; Xusi Han; Juan Esquivel-Rodriguez; Daisuke Kihara; Xiaofeng Yu; Neil J Bruce; Jonathan C Fuller; Rebecca C Wade; Ivan Anishchenko; Petras J Kundrotas; Ilya A Vakser; Kenichiro Imai; Kazunori Yamada; Toshiyuki Oda; Tsukasa Nakamura; Kentaro Tomii; Chiara Pallara; Miguel Romero-Durana; Brian Jiménez-García; Iain H Moal; Juan Férnandez-Recio; Jong Young Joung; Jong Yun Kim; Keehyoung Joo; Jooyoung Lee; Dima Kozakov; Sandor Vajda; Scott Mottarella; David R Hall; Dmitri Beglov; Artem Mamonov; Bing Xia; Tanggis Bohnuud; Carlos A Del Carpio; Eichiro Ichiishi; Nicholas Marze; Daisuke Kuroda; Shourya S Roy Burman; Jeffrey J Gray; Edrisse Chermak; Luigi Cavallo; Romina Oliva; Andrey Tovchigrechko; Shoshana J Wodak

doi:10.1002/prot.25007

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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Journal article

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Peer reviewed

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Marc F Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, …

Proteins, structure, function, and bioinformatics, Vol.84 Suppl 1(S1), pp.323-348

09/2016

DOI: https://doi.org/10.1002/prot.25007

PMCID: 5030136

PMID: 27122118

Abstract

Algorithms

Amino Acid Motifs

Bacteria - chemistry

Binding Sites

Computational Biology - methods

Computational Biology - statistics & numerical data

Humans

International Cooperation

Internet

Models, Statistical

Molecular Docking Simulation

Molecular Dynamics Simulation

Protein Binding

Protein Conformation, alpha-Helical

Protein Conformation, beta-Strand

Protein Folding

Protein Interaction Domains and Motifs

Protein Multimerization

Protein Structure, Tertiary

Proteins - chemistry

Sequence Homology, Amino Acid

Software

Thermodynamics

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.

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Title: Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
Creators - without role: Marc F Lensink - University of Lille
Sameer Velankar - European Bioinformatics Institute
Andriy Kryshtafovych - University of California, Davis
Shen-You Huang - University of Missouri
Dina Schneidman-Duhovny - University of California, San Francisco
Andrej Sali - University of California, San Francisco
Joan Segura - Centro Nacional de Biotecnología
Narcis Fernandez-Fuentes - Institute of Biological, Environmental and Rural Sciences
Shruthi Viswanath - The University of Texas at Austin
Ron Elber - The University of Texas at Austin
Sergei Grudinin - Université Grenoble Alpes
Petr Popov - Université Grenoble Alpes
Emilie Neveu - Université Grenoble Alpes
Hasup Lee - Seoul National University
Minkyung Baek - Seoul National University
Sangwoo Park - Seoul National University
Lim Heo - Seoul National University
Gyu Rie Lee - Seoul National University
Chaok Seok - Seoul National University
Sanbo Qin - Florida State University
Huan-Xiang Zhou - Florida State University
David W Ritchie - Inria Nancy - Grand-Est research centre
Bernard Maigret - Lorraine Research Laboratory in Computer Science and its Applications
Marie-Dominique Devignes - Lorraine Research Laboratory in Computer Science and its Applications
Anisah Ghoorah - University of Mauritius
Mieczyslaw Torchala - The Francis Crick Institute
Raphaël A G Chaleil - The Francis Crick Institute
Paul A Bates - The Francis Crick Institute
Efrat Ben-Zeev - Weizmann Institute of Science
Miriam Eisenstein - Weizmann Institute of Science
Surendra S Negi - The University of Texas Medical Branch at Galveston
Zhiping Weng - University of Massachusetts Chan Medical School
Thom Vreven - University of Massachusetts Chan Medical School
Brian G Pierce - University of Massachusetts Chan Medical School
Tyler M Borrman - University of Massachusetts Chan Medical School
Jinchao Yu - Institute of Integrative Biology of the Cell
Françoise Ochsenbein - Institute of Integrative Biology of the Cell
Raphaël Guerois - Institute of Integrative Biology of the Cell
Anna Vangone - Utrecht University
João P G L M Rodrigues - Utrecht University
Gydo van Zundert - Utrecht University
Mehdi Nellen - Utrecht University
Li Xue - Utrecht University
Ezgi Karaca - Utrecht University
Adrien S J Melquiond - Utrecht University
Koen Visscher - Utrecht University
Panagiotis L Kastritis - Utrecht University
Alexandre M J J Bonvin - Utrecht University
Xianjin Xu - University of Missouri
Liming Qiu - University of Missouri
Chengfei Yan - University of Missouri
Jilong Li - University of Missouri
Zhiwei Ma - University of Missouri
Jianlin Cheng - University of Missouri
Xiaoqin Zou - University of Missouri
Yang Shen - Toyota Technological Institute at Chicago
Lenna X Peterson - Purdue University West Lafayette
Hyung-Rae Kim - Purdue University West Lafayette
Amit Roy - Purdue University West Lafayette
Xusi Han - Purdue University West Lafayette
Juan Esquivel-Rodriguez - Purdue University West Lafayette
Daisuke Kihara - Purdue University West Lafayette
Xiaofeng Yu - Heidelberg Institute for Theoretical Studies
Neil J Bruce - Heidelberg Institute for Theoretical Studies
Jonathan C Fuller - Heidelberg Institute for Theoretical Studies
Rebecca C Wade - Heidelberg Institute for Theoretical Studies
Ivan Anishchenko - University of Kansas
Petras J Kundrotas - University of Kansas
Ilya A Vakser - University of Kansas
Kenichiro Imai - Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
Kazunori Yamada - National Institute of Advanced Industrial Science and Technology
Toshiyuki Oda - Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
Tsukasa Nakamura - The University of Tokyo
Kentaro Tomii - National Institute of Advanced Industrial Science and Technology
Chiara Pallara - Barcelona Supercomputing Center
Miguel Romero-Durana - Barcelona Supercomputing Center
Brian Jiménez-García - Barcelona Supercomputing Center
Iain H Moal - Barcelona Supercomputing Center
Juan Férnandez-Recio - Barcelona Supercomputing Center
Jong Young Joung - Korea Institute for Advanced Study
Jong Yun Kim - Korea Institute for Advanced Study
Keehyoung Joo - Korea Institute for Advanced Study
Jooyoung Lee - Korea Institute for Advanced Study
Dima Kozakov - Boston University
Sandor Vajda - Boston University
Scott Mottarella - Boston University
David R Hall - Boston University
Dmitri Beglov - Boston University
Artem Mamonov - Boston University
Bing Xia - Boston University
Tanggis Bohnuud - Boston University
Carlos A Del Carpio - Kyoto Institute of Technology
Eichiro Ichiishi - International University of Health and Welfare
Nicholas Marze - Johns Hopkins University
Daisuke Kuroda - Johns Hopkins University
Shourya S Roy Burman - Johns Hopkins University
Jeffrey J Gray - Johns Hopkins University
Edrisse Chermak - King Abdullah University of Science and Technology
Luigi Cavallo - King Abdullah University of Science and Technology
Romina Oliva - Parthenope University of Naples
Andrey Tovchigrechko - J. Craig Venter Institute
Shoshana J Wodak - VIB Structural Biology Research Center, VUB Pleinlaan 2, Brussels, 1050, Belgium. shoshana.wodak@gmail.com
Publication Details: Proteins, structure, function, and bioinformatics, Vol.84 Suppl 1(S1), pp.323-348
Grant note: R01 GM109980 / NIGMS NIH HHS R01 GM100482 / NIGMS NIH HHS R01 GM058187 / NIGMS NIH HHS R01 GM093123 / NIGMS NIH HHS P41 GM109824 / NIGMS NIH HHS R35 GM118078 / NIGMS NIH HHS BBS/E/W/10962A01D / Biotechnology and Biological Sciences Research Council Cancer Research UK R01 GM097528 / NIGMS NIH HHS R01 GM093147 / NIGMS NIH HHS R01 GM074255 / NIGMS NIH HHS R01 GM061867 / NIGMS NIH HHS R01 GM078221 / NIGMS NIH HHS R01 GM083960 / NIGMS NIH HHS
Identifiers: 9944219608331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article