Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 84, Issue -, Pages 323-348Publisher
WILEY
DOI: 10.1002/prot.25007
Keywords
CAPRI; CASP; oligomer state; blind prediction; protein interaction; protein docking
Categories
Funding
- NIH [R01 GM083960, P41 GM109824, GM058187, R01 GM061867, R01 GM093147, R01 GM078221, R01GM109980, R01GM094123, R01 GM097528, R01GM074255]
- Biotechnology and Biological Sciences Research Council [BBS/E/W/10962A01D]
- Research Councils UK Academic Fellowship program
- Cancer Research UK
- Klaus Tschira Foundation
- Japan Agency for Medical Research and Development
- Agence Nationale de la Recherche [ANR-11-MONU-0006, 2013R1A2A1A09012229, 2008-0061987]
- BIP [ANR-IAB-2011-16-BIP: BIP]
- H Marie Sklodowska-Curie Individual Fellowship [659025-BAP]
- Netherlands Organization for Scientific Research Veni [722.014.005]
- National Science Foundation [CAREER Award DBI0953839, CCF1546278, NSF IIS1319551, NSF DBI1262189, NSF IOS1127027, NSF DBI1262621, NSF DBI 1458509, NSF AF 1527292]
- EU [FP7 604102 (HBP)]
- BMBF [0315749]
- Spanish Ministry of Economy and Competitiveness [BIO2013-48213-R]
- European Union [FP7/2007-2013 REA PIEF-GA-2012-327899]
- National Institute of Supercomputing and Networking [KSC-2014-C3-01]
- US-Israel BSF [2009418]
- Regione Campania [LR5-AF2008]
- Marie Curie Actions (MSCA) [659025] Funding Source: Marie Curie Actions (MSCA)
- Agence Nationale de la Recherche (ANR) [ANR-11-MONU-0006] Funding Source: Agence Nationale de la Recherche (ANR)
- Direct For Biological Sciences
- Div Of Biological Infrastructure [0953839, 1147082] Funding Source: National Science Foundation
- Division of Computing and Communication Foundations
- Direct For Computer & Info Scie & Enginr [1546278] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1458509, 1262621] Funding Source: National Science Foundation
- Biotechnology and Biological Sciences Research Council [BBS/E/W/10962A01D] Funding Source: researchfish
- Cancer Research UK [10748] Funding Source: researchfish
- BBSRC [BBS/E/W/10962A01D] Funding Source: UKRI
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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 homo-tetramers, 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. (C) 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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