Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
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.
University Lille, CNRS UMR8576 UGSF, Lille, F-59000, France. marc.lensink@univ-lille1.fr.
Marc F
0000-0003-3957-9470
MF
Lensink
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
Sameer
S
Velankar
Genome Center, University of California, Davis, California, 95616.
Andriy
A
Kryshtafovych
Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri, Columbia, Missouri, 65211.
Shen-You
SY
Huang
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.
Dina
D
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.|California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, 94158.
Andrej
A
Sali
GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), Madrid, 28049, Spain.
Joan
J
Segura
Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY233FG, United Kingdom.
Narcis
N
Fernandez-Fuentes
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.
Shruthi
S
Viswanath
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.
Ron
R
Elber
LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France.|INRIA, Grenoble, 38000, France.
Sergei
S
Grudinin
LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France.|INRIA, Grenoble, 38000, France.|Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
Petr
P
Popov
LJK, University Grenoble Alpes, CNRS, Grenoble, 38000, France.|INRIA, Grenoble, 38000, France.
Emilie
E
Neveu
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Hasup
H
Lee
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Minkyung
M
Baek
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Sangwoo
S
Park
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Lim
L
Heo
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Gyu
G
Rie Lee
Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.
Chaok
C
Seok
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306, USA.
Sanbo
S
Qin
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306, USA.
Huan-Xiang
HX
Zhou
INRIA Nancy-Grand Est, Villers-lès-Nancy, 54600, France.
David W
DW
Ritchie
CNRS, LORIA, Campus Scientifique, BP 239, Vandœuvre-lès-Nancy, 54506, France.
Bernard
B
Maigret
CNRS, LORIA, Campus Scientifique, BP 239, Vandœuvre-lès-Nancy, 54506, France.
Marie-Dominique
MD
Devignes
Department of Computer Science and Engineering, University of Mauritius, Reduit, Mauritius.
Anisah
A
Ghoorah
Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.
Mieczyslaw
M
Torchala
Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.
Raphaël A G
RA
Chaleil
Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, WC2A 3LY, United Kingdom.
Paul A
PA
Bates
G-INCPM, Weizmann Institute of Science, Rehovot, 7610001, Israel.
Efrat
E
Ben-Zeev
Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.
Miriam
M
Eisenstein
Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas, 77555-0857.
Surendra S
SS
Negi
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Zhiping
Z
Weng
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Thom
T
Vreven
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Brian G
BG
Pierce
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.
Tyler M
TM
Borrman
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France.
Jinchao
J
Yu
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France.
Françoise
F
Ochsenbein
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, 91191, France.
Raphaël
R
Guerois
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Anna
A
Vangone
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
João P G L M
JP
Rodrigues
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Gydo
G
van Zundert
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Mehdi
M
Nellen
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Li
L
Xue
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Ezgi
E
Karaca
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Adrien S J
AS
Melquiond
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Koen
K
Visscher
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Panagiotis L
PL
Kastritis
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
Alexandre M J J
0000-0001-7369-1322
AM
Bonvin
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.
Xianjin
X
Xu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.
Liming
L
Qiu
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.|Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
Chengfei
C
Yan
Department of Computer Science, University of Missouri, Columbia, Missouri, 65211.
Jilong
J
Li
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.|Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211.
Zhiwei
Z
Ma
Department of Computer Science, University of Missouri, Columbia, Missouri, 65211.|Informatics Institute, University of Missouri, Columbia, Missouri, 65211.
Jianlin
J
Cheng
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.
Xiaoqin
X
Zou
Toyota Technological Institute at Chicago, 6045 S Kenwood Avenue, Chicago, Illinois, 60637.
Yang
0000-0003-4728-1973
Y
Shen
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.
Lenna X
LX
Peterson
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.
Hyung-Rae
HR
Kim
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.
Amit
A
Roy
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.
Xusi
X
Han
Department of Computer Science, Purdue University, West Lafayette, IN, USA, 47907.
Juan
J
Esquivel-Rodriguez
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.|Department of Computer Science, Purdue University, West Lafayette, IN, USA, 47907.
Daisuke
D
Kihara
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Xiaofeng
X
Yu
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Neil J
NJ
Bruce
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Jonathan C
JC
Fuller
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.
Rebecca C
RC
Wade
Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047.
Ivan
I
Anishchenko
Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047.
Petras J
PJ
Kundrotas
Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047.|Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66047.
Ilya A
IA
Vakser
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan.
Kenichiro
K
Imai
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan.
Kazunori
K
Yamada
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-Ku, Japan.
Toshiyuki
T
Oda
Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
Tsukasa
T
Nakamura
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.
Kentaro
K
Tomii
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
Chiara
C
Pallara
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
Miguel
M
Romero-Durana
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
Brian
B
Jiménez-García
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
Iain H
IH
Moal
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, C/Jordi Girona 29, Barcelona, 08034, Spain.
Juan
J
Férnandez-Recio
Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
Jong Young
JY
Joung
Center for in-Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
Jong Yun
JY
Kim
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.
Keehyoung
K
Joo
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.
Jooyoung
J
Lee
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Dima
D
Kozakov
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.|Department of Chemistry, Boston University, Boston, Massachusetts.
Sandor
S
Vajda
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Scott
S
Mottarella
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
David R
DR
Hall
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Dmitri
D
Beglov
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Artem
A
Mamonov
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Bing
B
Xia
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Tanggis
T
Bohnuud
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.
Carlos A
CA
Del Carpio
International University of Health and Welfare Hospital (IUHW Hospital), Asushiobara-City, Tochigi Prefecture, 329-2763, Japan.
Eichiro
E
Ichiishi
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.
Nicholas
N
Marze
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.
Daisuke
D
Kuroda
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.
Shourya S
SS
Roy Burman
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.|Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, 21218.
Jeffrey J
0000-0001-6380-2324
JJ
Gray
King Abdullah University of Science and Technology, Saudi Arabia.
Edrisse
E
Chermak
King Abdullah University of Science and Technology, Saudi Arabia.
Luigi
L
Cavallo
University of Naples "Parthenope", Napoli, Italy.
Romina
R
Oliva
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, 20850.
Andrey
A
Tovchigrechko
Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. shoshana.wodak@gmail.com.|VIB Structural Biology Research Center, VUB Pleinlaan 2, Brussels, 1050, Belgium. shoshana.wodak@gmail.com.
Shoshana J
SJ
Wodak
D000465:Algorithms; D020816:Amino Acid Motifs; D001419:Bacteria / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D006801:Humans; D007391:International Cooperation; D020407:Internet; D015233:Models, Statistical; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013816:Thermodynamics
D011506:Proteins
CAPRI; CASP; blind prediction; oligomer state; protein docking; protein interaction