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

TitlePrediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Publication TypeJournal Article
Year of Publication2016
AuthorsLensink, M. F., S. Velankar, A. Kryshtafovych, S-Y. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, et al.
JournalProteins
Volume84 Suppl 1
Pagination323-48
Date Published2016 Sep
ISSN1097-0134
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. © 2016 Wiley Periodicals, Inc.

DOI10.1002/prot.25007
Alternate JournalProteins
PubMed ID27122118
PubMed Central IDPMC5030136
Grant ListR01 GM074255 / GM / NIGMS NIH HHS / United States
R01 GM109980 / GM / NIGMS NIH HHS / United States
R01 GM078221 / GM / NIGMS NIH HHS / United States
R01 GM058187 / GM / NIGMS NIH HHS / United States
R01 GM093123 / GM / NIGMS NIH HHS / United States
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