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Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25.

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Author information

1
University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
3
Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
4
CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.
5
Institut Universitaire de France (IUF), Paris, France.
6
Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.
7
Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
8
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
9
Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
10
Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland.
11
Polish Academy of Sciences, Institute of Physics, Warsaw, Poland.
12
Polish Academy of Sciences, Institute of Computer Science, Warsaw, Poland.
13
School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea.
14
Department of Computer Science, UC Davis, Davis, California.
15
Department of Computer Science, ETH, Zurich, Switzerland.
16
Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
17
School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
18
Barcelona Supercomputing Center (BSC), Barcelona, Spain.
19
Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain.
20
Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain.
21
Department of Computer Science, Purdue University, West Lafayette, Indiana.
22
Department of Biological Sciences, Purdue University, West Lafayette, Indiana.
23
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.
24
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
25
Department of Chemistry, Boston University, Boston, Massachusetts.
26
University of Lorraine, CNRS, Inria, LORIA, Nancy, France.
27
Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
28
Department of Sciences and Technologies, University of Naples "Parthenope", Napoli, Italy.
29
Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas.
30
Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
31
Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
32
School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
33
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
34
Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
35
Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
36
University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.
37
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland.
38
Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.
39
Department of Computer Science, University of Missouri, Columbia, Missouri.
40
Informatics Institute, University of Missouri, Columbia, Missouri.
41
Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.
42
Department of Biochemistry, University of Missouri, Columbia, Missouri.
43
Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
44
VIB Structural Biology Research Center, VUB, Brussels, Belgium.

Abstract

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

KEYWORDS:

CAPRI; CASP; blind prediction; docking; oligomeric state; protein assemblies; protein complexes; protein-protein interaction; template-based modeling

PMID:
31612567
DOI:
10.1002/prot.25838

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