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Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JPGLM, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 2016; 84 Suppl 1:323-48. [PMID: 27122118 PMCID: PMC5030136 DOI: 10.1002/prot.25007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 12/30/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022]
Abstract
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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Affiliation(s)
- Marc F Lensink
- University Lille, CNRS UMR8576 UGSF, Lille, F-59000, France.
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | | | - Shen-You Huang
- Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, Missouri, 65211
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, 94158
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, 94158
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158
- California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, 94158
| | - Joan Segura
- GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), Madrid, 28049, Spain
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY233FG, United Kingdom
| | - Shruthi Viswanath
- Department of Computer Science, University of Texas at Austin, Austin, Texas, 78712
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712
| | - Sergei Grudinin
- LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France
- INRIA, Grenoble, 38000, France
| | - Petr Popov
- LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France
- INRIA, Grenoble, 38000, France
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Emilie Neveu
- LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France
- INRIA, Grenoble, 38000, France
| | - Hasup Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Minkyung Baek
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Sangwoo Park
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Lim Heo
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Gyu Rie Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306, USA
| | | | - Bernard Maigret
- CNRS, LORIA, Campus Scientifique, BP 239, Vandœuvre-lès-Nancy, 54506, France
| | | | - Anisah Ghoorah
- Department of Computer Science and Engineering, University of Mauritius, Reduit, Mauritius
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom
| | - Raphaël A G Chaleil
- Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom
| | - Paul A Bates
- Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom
| | - Efrat Ben-Zeev
- G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Miriam Eisenstein
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Surendra S Negi
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas, 77555-0857
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Brian G Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Tyler M Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France
| | - Anna Vangone
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - João P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Gydo van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Mehdi Nellen
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Li Xue
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Ezgi Karaca
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Adrien S J Melquiond
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Koen Visscher
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211
| | - Chengfei Yan
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211
| | - Jilong Li
- Department of Computer Science, University of Missouri, Columbia, Missouri, 65211
| | - Zhiwei Ma
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, Columbia, Missouri, 65211
- Informatics Institute, University of Missouri, Columbia, Missouri, 65211
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211
- Informatics Institute, University of Missouri, Columbia, Missouri, 65211
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211
| | - Yang Shen
- Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, Illinois, 60637
| | - Lenna X Peterson
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Hyung-Rae Kim
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Amit Roy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, Montano 59840
| | - Xusi Han
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | | | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
- Department of Computer Science, Purdue University, West Lafayette, IN, USA, 47907
| | - Xiaofeng Yu
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Jonathan C Fuller
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Ivan Anishchenko
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047
| | - Petras J Kundrotas
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047
| | - Ilya A Vakser
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66047
| | - Kenichiro Imai
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
| | - Kazunori Yamada
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
| | - Toshiyuki Oda
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
| | - Tsukasa Nakamura
- Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan
| | - Kentaro Tomii
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan
- Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan
| | - Chiara Pallara
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain
| | - Miguel Romero-Durana
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain
| | - Brian Jiménez-García
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain
| | - Iain H Moal
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain
| | - Juan Férnandez-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain
| | - Jong Young Joung
- Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea
| | - Jong Yun Kim
- Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea
| | - Keehyoung Joo
- Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, 130-722, Korea
| | - Jooyoung Lee
- Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea
- School of Computational Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - Scott Mottarella
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - David R Hall
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Artem Mamonov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Tanggis Bohnuud
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Carlos A Del Carpio
- Institute of Biological Diversity, International Pacific Institute of Indiana, Bloomington, Indiana, 47401
- Drosophila Genetic Resource Center, Kyoto Institute of Technology, Ukyo-Ku, 616-8354, Japan
| | - Eichiro Ichiishi
- International University of Health and Welfare Hospital (IUHW Hospital), Asushiobara-City, Tochigi Prefecture, 329-2763, Japan
| | - Nicholas Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, 21218
| | - Edrisse Chermak
- King Abdullah University of Science and Technology, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology, Saudi Arabia
| | - Romina Oliva
- University of Naples "Parthenope", Napoli, Italy
| | - Andrey Tovchigrechko
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, 20850
| | - Shoshana J Wodak
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- VIB Structural Biology Research Center, VUB Pleinlaan 2, Brussels, 1050, Belgium.
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