Assessment of protein assembly prediction in CASP13
Abstract
We present here the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should anticipate more integrated approaches where subunits are modeled in the context of the assemblies they form.
- Authors:
-
[1];
[2];
[3];
[1]
- Univ. of California, San Diego, CA (United States)
- European Molecular Biology Lab., Cambridge (United Kingdom)
- Univ. of California, Davis, CA (United States)
- Publication Date:
- Research Org.:
- Rutgers Univ., New Brunswick, NJ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of General Medical Sciences
- OSTI Identifier:
- 1601671
- Grant/Contract Number:
- SC0019749; GM100482
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proteins
- Additional Journal Information:
- Journal Volume: 87; Journal Issue: 12; Journal ID: ISSN 0887-3585
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; CASP; protein assembly; protein interfaces; structure prediction
Citation Formats
Guzenko, Dmytro, Lafita, Aleix, Monastyrskyy, Bohdan, Kryshtafovych, Andriy, and Duarte, Jose M. Assessment of protein assembly prediction in CASP13. United States: N. p., 2019.
Web. doi:10.1002/prot.25795.
Guzenko, Dmytro, Lafita, Aleix, Monastyrskyy, Bohdan, Kryshtafovych, Andriy, & Duarte, Jose M. Assessment of protein assembly prediction in CASP13. United States. https://doi.org/10.1002/prot.25795
Guzenko, Dmytro, Lafita, Aleix, Monastyrskyy, Bohdan, Kryshtafovych, Andriy, and Duarte, Jose M. Fri .
"Assessment of protein assembly prediction in CASP13". United States. https://doi.org/10.1002/prot.25795. https://www.osti.gov/servlets/purl/1601671.
@article{osti_1601671,
title = {Assessment of protein assembly prediction in CASP13},
author = {Guzenko, Dmytro and Lafita, Aleix and Monastyrskyy, Bohdan and Kryshtafovych, Andriy and Duarte, Jose M.},
abstractNote = {We present here the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should anticipate more integrated approaches where subunits are modeled in the context of the assemblies they form.},
doi = {10.1002/prot.25795},
journal = {Proteins},
number = 12,
volume = 87,
place = {United States},
year = {Fri Aug 02 00:00:00 EDT 2019},
month = {Fri Aug 02 00:00:00 EDT 2019}
}
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Figures / Tables:
FIGURE 1: Score correlations. A heat map with correlations among all relevant scores used in the predictioncenter.org web site. The “local” block of scores captures interface features, the “global” block captures features of the whole assembly.
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Works referenced in this record:
The Application of the oil Turbine type of Ultracentrifuge to the Study of the Stability Region of Carbon Monoxide-Hemoglobin
journal, November 1927
- Svedberg, The; Nichols, J. B.
- Journal of the American Chemical Society, Vol. 49, Issue 11
Structural Symmetry and Protein Function
journal, June 2000
- Goodsell, David S.; Olson, Arthur J.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1
Dynamic dissociating homo-oligomers and the control of protein function
journal, March 2012
- Selwood, Trevor; Jaffe, Eileen K.
- Archives of Biochemistry and Biophysics, Vol. 519, Issue 2
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
journal, November 2010
- Hashimoto, K.; Panchenko, A. R.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 47
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018
- Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
- Nucleic Acids Research, Vol. 47, Issue D1
Inside a living cell
journal, January 1991
- Goodsell, David S.
- Trends in Biochemical Sciences, Vol. 16
Protein folding via binding and vice versa
journal, August 1998
- Tsai, Chung-Jung; Xu, Dong; Nussinov, Ruth
- Folding and Design, Vol. 3, Issue 4
NEW EMBO MEMBER'S REVIEW: Diversity of protein-protein interactions
journal, July 2003
- Nooren, I. M. A.
- The EMBO Journal, Vol. 22, Issue 14
A survey of protein–protein complex crystallizations
journal, May 2006
- Radaev, Sergei; Li, Sean; Sun, Peter D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 6
Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies
journal, June 2019
- Ognjenović, Jana; Grisshammer, Reinhard; Subramaniam, Sriram
- Annual Review of Biomedical Engineering, Vol. 21, Issue 1
Meeting review: the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13–16, 1996
journal, April 1997
- Dunbrack, Roland L.; Gerloff, Dietlind L.; Bower, Michael
- Folding and Design, Vol. 2, Issue 2
Assessment of CASP7 structure predictions for template free targets
journal, January 2007
- Jauch, Ralf; Yeo, Hock Chuan; Kolatkar, Prasanna R.
- Proteins: Structure, Function, and Bioinformatics, Vol. 69, Issue S8
Assessment of template based protein structure predictions in CASP9
journal, January 2011
- Mariani, Valerio; Kiefer, Florian; Schmidt, Tobias
- Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue S10
The challenge of modeling protein assemblies: the CASP12-CAPRI experiment
journal, November 2017
- Lensink, Marc F.; Velankar, Sameer; Baek, Minkyung
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Assessment of protein assembly prediction in CASP12
journal, November 2017
- Lafita, Aleix; Bliven, Spencer; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods
journal, November 2017
- Abriata, Luciano A.; Tamò, Giorgio E.; Monastyrskyy, Bohdan
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age
journal, November 2017
- Schaarschmidt, Joerg; Monastyrskyy, Bohdan; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Critical assessment of methods of protein structure prediction (CASP)-Round XII
journal, December 2017
- Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts
journal, October 2015
- Capitani, Guido; Duarte, Jose M.; Baskaran, Kumaran
- Bioinformatics, Vol. 32, Issue 4
Automated evaluation of quaternary structures from protein crystals
journal, April 2018
- Bliven, Spencer; Lafita, Aleix; Parker, Althea
- PLOS Computational Biology, Vol. 14, Issue 4
Stock-based detection of protein oligomeric states in jsPISA
journal, April 2015
- Krissinel, Eugene
- Nucleic Acids Research, Vol. 43, Issue W1
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
journal, July 2018
- Zimmermann, Lukas; Stephens, Andrew; Nam, Seung-Zin
- Journal of Molecular Biology, Vol. 430, Issue 15
Principles and characteristics of biological assemblies in experimentally determined protein structures
journal, April 2019
- Xu, Qifang; Dunbrack, Roland L.
- Current Opinion in Structural Biology, Vol. 55
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
journal, August 2013
- Mariani, Valerio; Biasini, Marco; Barbato, Alessandro
- Bioinformatics, Vol. 29, Issue 21
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
journal, September 2017
- Bertoni, Martino; Kiefer, Florian; Biasini, Marco
- Scientific Reports, Vol. 7, Issue 1
BioJava 5: A community driven open-source bioinformatics library
journal, February 2019
- Lafita, Aleix; Bliven, Spencer; Prlić, Andreas
- PLOS Computational Biology, Vol. 15, Issue 2
Evaluation of template-based models in CASP8 with standard measures
journal, January 2009
- Cozzetto, Domenico; Kryshtafovych, Andriy; Fidelis, Krzysztof
- Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue S9
CASP13 target classification into tertiary structure prediction categories
journal, July 2019
- Kinch, Lisa N.; Kryshtafovych, Andriy; Monastyrskyy, Bohdan
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
CATH: an expanded resource to predict protein function through structure and sequence
journal, November 2016
- Dawson, Natalie L.; Lewis, Tony E.; Das, Sayoni
- Nucleic Acids Research, Vol. 45, Issue D1
Assessing the accuracy of contact predictions in CASP13
journal, August 2019
- Shrestha, Rojan; Fajardo, Eduardo; Gil, Nelson
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
Optimal contact definition for reconstruction of Contact Maps
journal, May 2010
- Duarte, Jose M.; Sathyapriya, Rajagopal; Stehr, Henning
- BMC Bioinformatics, Vol. 11, Issue 1
Defining an Essence of Structure Determining Residue Contacts in Proteins
journal, December 2009
- Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning
- PLoS Computational Biology, Vol. 5, Issue 12
Sequence co-evolution gives 3D contacts and structures of protein complexes
journal, September 2014
- Hopf, Thomas A.; Schärfe, Charlotta P. I.; Rodrigues, João P. G. L. M.
- eLife, Vol. 3
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
journal, May 2014
- Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David
- eLife, Vol. 3
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
journal, May 2018
- Quignot, Chloé; Rey, Julien; Yu, Jinchao
- Nucleic Acids Research, Vol. 46, Issue W1
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy
journal, February 2018
- Ogorzalek, Tadeusz L.; Hura, Greg L.; Belsom, Adam
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences
journal, August 2019
- Hura, Greg L.; Hodge, Curtis D.; Rosenberg, Daniel
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
SWISS-MODEL: homology modelling of protein structures and complexes
journal, May 2018
- Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan
- Nucleic Acids Research, Vol. 46, Issue W1
Protein structure prediction and analysis using the Robetta server
journal, July 2004
- Kim, D. E.; Chivian, D.; Baker, D.
- Nucleic Acids Research, Vol. 32, Issue Web Server
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12
journal, December 2017
- Haas, Jürgen; Barbato, Alessandro; Behringer, Dario
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993
- Šali, Andrej; Blundell, Tom L.
- Journal of Molecular Biology, Vol. 234, Issue 3
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy
journal, February 2018
- Ogorzalek, Tadeusz L.; Hura, Greg L.; Belsom, Adam
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Inside a living cell
journal, January 1991
- Goodsell, David S.
- Trends in Biochemical Sciences, Vol. 16
NEW EMBO MEMBER'S REVIEW: Diversity of protein-protein interactions
journal, July 2003
- Nooren, I. M. A.
- The EMBO Journal, Vol. 22, Issue 14
Defining an Essence of Structure Determining Residue Contacts in Proteins
journal, December 2009
- Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning
- PLoS Computational Biology, Vol. 5, Issue 12
Works referencing / citing this record:
Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results
journal, August 2019
- Kryshtafovych, Andriy; Malhotra, Sony; Monastyrskyy, Bohdan
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
Critical assessment of methods of protein structure prediction (CASP)—Round XIII
journal, August 2019
- Kryshtafovych, Andriy; Schwede, Torsten; Topf, Maya
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
journal, August 2019
- Lensink, Marc F.; Brysbaert, Guillaume; Nadzirin, Nurul
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12
Template‐based modeling of diverse protein interactions in CAPRI rounds 38‐45
journal, November 2019
- Dapkūnas, Justas; Kairys, Visvaldas; Olechnovič, Kliment
- Proteins: Structure, Function, and Bioinformatics, Vol. 88, Issue 8
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