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Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

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

Author information

1
University Lille, CNRS UMR8576 UGSF, Lille, F-59000, France. marc.lensink@univ-lille1.fr.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
3
Genome Center, University of California, Davis, California, 95616.
4
Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, Missouri, 65211.
5
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, 94158.
6
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158.
7
California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, 94158.
8
GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), Madrid, 28049, Spain.
9
Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY233FG, United Kingdom.
10
Department of Computer Science, University of Texas at Austin, Austin, Texas, 78712.
11
Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712.
12
Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712.
13
LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France.
14
INRIA, Grenoble, 38000, France.
15
Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
16
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
17
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306, USA.
18
INRIA Nancy-Grand Est, Villers-lès-Nancy, 54600, France.
19
CNRS, LORIA, Campus Scientifique, BP 239, Vandœuvre-lès-Nancy, 54506, France.
20
Department of Computer Science and Engineering, University of Mauritius, Reduit, Mauritius.
21
Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.
22
G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel.
23
Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.
24
Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas, 77555-0857.
25
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
26
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France.
27
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
28
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.
29
Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
30
Department of Computer Science, University of Missouri, Columbia, Missouri, 65211.
31
Informatics Institute, University of Missouri, Columbia, Missouri, 65211.
32
Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211.
33
Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, Illinois, 60637.
34
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.
35
Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, Montano 59840.
36
Department of Computer Science, Purdue University, West Lafayette, IN, USA, 47907.
37
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
38
Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
39
Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
40
Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047.
41
Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66047.
42
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan.
43
Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
44
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
45
Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
46
Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
47
School of Computational Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
48
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
49
Department of Chemistry, Boston University, Boston, Massachusetts.
50
Institute of Biological Diversity, International Pacific Institute of Indiana, Bloomington, Indiana, 47401.
51
Drosophila Genetic Resource Center, Kyoto Institute of Technology, Ukyo-Ku, 616-8354, Japan.
52
International University of Health and Welfare Hospital (IUHW Hospital), Asushiobara-City, Tochigi Prefecture, 329-2763, Japan.
53
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.
54
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, 21218.
55
King Abdullah University of Science and Technology, Saudi Arabia.
56
University of Naples "Parthenope", Napoli, Italy.
57
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, 20850.
58
Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. shoshana.wodak@gmail.com.
59
VIB Structural Biology Research Center, VUB Pleinlaan 2, Brussels, 1050, Belgium. shoshana.wodak@gmail.com.

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.

KEYWORDS:

CAPRI; CASP; blind prediction; oligomer state; protein docking; protein interaction

PMID:
27122118
PMCID:
PMC5030136
DOI:
10.1002/prot.25007
[Indexed for MEDLINE]
Free PMC Article

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