Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment
Marc F. Lensink
(1)
,
Sameer Velankar
(2)
,
Andriy Kryshtafovych
(3)
,
Shen-You Huang
(4)
,
Dina Schneidman-Duhovy
(5)
,
Andrej Sali
(5)
,
Joan Segura
(6)
,
Narcis Fernandez-Fuentes
(7)
,
Shruthi Viswanath
(8, 9)
,
Ron Elber
(8, 10)
,
Sergei Grudinin
(11)
,
Petr Popov
(12, 11)
,
Emilie Neveu
(11)
,
Hasup Lee
(13)
,
Minkyung Baek
(13)
,
Sangwoo Park
(13)
,
Lim Heo
(13)
,
Gyu Rie Lee
(13)
,
Chaok Seok
(13)
,
Sanbo Qin
(14)
,
Huan-Xiang Zhou
(14)
,
David W. Ritchie
(15)
,
Bernard Maigret
(15)
,
Marie-Dominique Devignes
(15)
,
Anisah Ghoorah
(16)
,
Mieczyslaw Torchala
(17)
,
Raphaël A.G. Chaleil
(17)
,
Paul A Bates
(17)
,
Efrat Ben-Zeev
(18)
,
Miriam Eisenstein
(19)
,
Surendra Negi S.
(20)
,
Thom Vreven
(21)
,
Brian G Pierce
(21)
,
Tyler M. Borrman
(21)
,
Jinchao Yu
(21)
,
Françoise Ochsenbein
(22, 23)
,
Zhiping Weng
(21)
,
Raphaël Guérois
(22, 23)
,
Anna Vangone
(24)
,
João P.G.L.M. Rodrigues
(24)
,
Gydo van Zundert
(24)
,
Mehdi Nellen
(24)
,
Li Xue
(24)
,
Ezgi Karaca
(24)
,
Adrien S. J. Melquiond
(24)
,
Koen Visscher
(24)
,
Panagiotis L Kastritis
(24)
,
Alexandre M. J. J. Bonvin
(24)
,
Xianjin Xu
(24)
,
Liming Qiu
(24)
,
Chengfei Yan
(25, 24)
,
Jilong Li
(26)
,
Zhiwei Ma
(24, 25)
,
Jianlin Cheng
(26, 27)
,
Xiaoqin Zou
(24, 25, 27, 28)
,
Yang Sheng
(29)
,
Lenna X. Peterson
(30)
,
Hyung-Rae Kim
(30)
,
Amit Roy
(31, 30)
,
Xusi Han
(30)
,
Juan Esquivel-Rodríguez
(32, 33)
,
Daisuke Kihara
(30, 33)
,
Xiaofeng Yu
(32)
,
Neil J. Bruce
(32)
,
Jonathan C. Fuller
(32)
,
Rebbecca C. Wade
(34, 32, 35)
,
Ivan Anishchenko
(36)
,
Petras J. Kundrotas
(36)
,
Ilya A. Vakser
(36, 37)
,
Kenichiro Imai
(37)
,
Kazunori Yamada
(37)
,
Toshiyuki Oda
(37)
,
Tsukasa Nakamura
(38)
,
Kentaro Tomii
(37, 38)
,
Chiara Pallara
(39)
,
Miguel Romero-Durana
(39)
,
Brian Jiménez-García
(39)
,
Iain H Moal
(40)
,
Juan Fernández-Recio
(40)
,
Jong Young Joung
(41)
,
Jong Yun Kim
(41)
,
Keehyoung Joo
(41, 42)
,
Jooyoung Lee
(41, 42)
,
Dima Kozakov
(43)
,
Sandor Vajda
(43, 44)
,
Scott Mottarella
(43)
,
David R. Hall
(43)
,
Dmitri Beglov
(43)
,
Artem Mamonov
(43)
,
Bing Xia
(43)
,
Tanggis Bohnuud
(43)
,
Carlos A. del Carpio
(45, 46)
,
Eichiro Ichiishi
(47)
,
Nicholas Marze
(48)
,
Daisuke Kuroda
(48)
,
Shourya S. Roy Burman
(48)
,
Jeffrey J Gray
(49, 48)
,
Edrisse Chermak
(50)
,
Luigi Cavallo
(50)
,
Romina Oliva
(51)
,
Andrey Tovchigrechko
(52)
,
Shoshana J Wodak
(53)
1
IRI -
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq]
2 EMBL-EBI - European Bioinformatics Institute [Hinxton]
3 Genome Center [UC Davis]
4 Mizzou - University of Missouri [Columbia]
5 Department of Bioengineering and Therapeutic Sciences
6 GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit
7 IBERS - Institute of Biological, Environmental and Rural Sciences
8 ICES - Institute for Computational Engineering and Sciences [Austin]
9 Department of Computer Science
10 Department of Chemistry
11 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
12 MIPT - Moscow Institute of Physics and Technology [Moscow]
13 Department of Chemistry
14 FSU - Florida State University [Tallahassee]
15 CAPSID - Computational Algorithms for Protein Structures and Interactions
16 University of Mauritius
17 Biomolecular Modelling Laboratory [London]
18 G-INCPM
19 Chemical Research Support [Rehovot]
20 Sealy Center for Structural Biology and Molecular Biophysics
21 Program in Bioinformatics and Integrative Biology [Worcester]
22 I2BC - Institut de Biologie Intégrative de la Cellule
23 AMIG - Assemblage moléculaire et intégrité du génome
24 Bijvoet Center for Biomolecular Research [Utrecht]
25 Dalton Cardiovascular Research Center [Columbia]
26 Department of Computer Science [Columbia]
27 Department of Computer Science
28 Informatics Intitute
29 Department of Biochemistry, University of Missouri
30 TTIC - Toyota Technological Institute at Chicago [Chicago]
31 Department of Biological Sciences [Lafayette IN]
32 Department of Computer Science [Purdue]
33 Bioinformatics and Computational Biosciences Branch
34 Molecular and Cellular Modeling Group
35 ZMBH - Center for Molecular Biology - Zentrum für Molekulare Biologie [Heidelberg, Germany]
36 IWR - Interdisciplinary Center for Scientific Computing
37 Department of Molecular Biosciences [Lawrence]
38 CBRC - Computational Biology Research Center
39 Graduate School of Frontier Sciences
40 Joint BSC-CRG-IRB Research Program in Computational Biology
41 Center for In-Silico Protein Science
42 Center for Advanced Computation
43 Department of Biomedical Engineering [Boston]
44 Department of Chemistry
45 Institute of Biological Diversity
46 Drosophila Genetic Resource Center
47 IUHW Hospital - International University of Health and Welfare Hospital
48 Department of Chemical and Biomolecular Engineering [Baltimore]
49 Program in Molecular Biophysics [Baltimore]
50 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
51 University of Naples Federico II = Università degli studi di Napoli Federico II
52 J. Craig Venter Institute
53 VIB-VUB Center for Structural Biology [Bruxelles]
2 EMBL-EBI - European Bioinformatics Institute [Hinxton]
3 Genome Center [UC Davis]
4 Mizzou - University of Missouri [Columbia]
5 Department of Bioengineering and Therapeutic Sciences
6 GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit
7 IBERS - Institute of Biological, Environmental and Rural Sciences
8 ICES - Institute for Computational Engineering and Sciences [Austin]
9 Department of Computer Science
10 Department of Chemistry
11 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
12 MIPT - Moscow Institute of Physics and Technology [Moscow]
13 Department of Chemistry
14 FSU - Florida State University [Tallahassee]
15 CAPSID - Computational Algorithms for Protein Structures and Interactions
16 University of Mauritius
17 Biomolecular Modelling Laboratory [London]
18 G-INCPM
19 Chemical Research Support [Rehovot]
20 Sealy Center for Structural Biology and Molecular Biophysics
21 Program in Bioinformatics and Integrative Biology [Worcester]
22 I2BC - Institut de Biologie Intégrative de la Cellule
23 AMIG - Assemblage moléculaire et intégrité du génome
24 Bijvoet Center for Biomolecular Research [Utrecht]
25 Dalton Cardiovascular Research Center [Columbia]
26 Department of Computer Science [Columbia]
27 Department of Computer Science
28 Informatics Intitute
29 Department of Biochemistry, University of Missouri
30 TTIC - Toyota Technological Institute at Chicago [Chicago]
31 Department of Biological Sciences [Lafayette IN]
32 Department of Computer Science [Purdue]
33 Bioinformatics and Computational Biosciences Branch
34 Molecular and Cellular Modeling Group
35 ZMBH - Center for Molecular Biology - Zentrum für Molekulare Biologie [Heidelberg, Germany]
36 IWR - Interdisciplinary Center for Scientific Computing
37 Department of Molecular Biosciences [Lawrence]
38 CBRC - Computational Biology Research Center
39 Graduate School of Frontier Sciences
40 Joint BSC-CRG-IRB Research Program in Computational Biology
41 Center for In-Silico Protein Science
42 Center for Advanced Computation
43 Department of Biomedical Engineering [Boston]
44 Department of Chemistry
45 Institute of Biological Diversity
46 Drosophila Genetic Resource Center
47 IUHW Hospital - International University of Health and Welfare Hospital
48 Department of Chemical and Biomolecular Engineering [Baltimore]
49 Program in Molecular Biophysics [Baltimore]
50 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
51 University of Naples Federico II = Università degli studi di Napoli Federico II
52 J. Craig Venter Institute
53 VIB-VUB Center for Structural Biology [Bruxelles]
Marc F. Lensink
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Andriy Kryshtafovych
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Sergei Grudinin
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David W. Ritchie
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Bernard Maigret
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Marie-Dominique Devignes
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Raphaël Guérois
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Xiaoqin Zou
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Daisuke Kihara
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Keehyoung Joo
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Dima Kozakov
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Sandor Vajda
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Daisuke Kuroda
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Edrisse Chermak
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Luigi Cavallo
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Résumé
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. This article is protected by copyright. All rights reserved.