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Method | Open Access

CHDOCK: a hierarchical docking approach for modeling C n symmetric homo-oligomeric complexes

Yumeng Yan1Sheng-You Huang1( )
Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
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Abstract

Protein–protein interactions are crucial in many biological processes. Therefore, determining the complex structure between proteins is valuable for understanding the molecular mechanism and developing drugs. Many proteins like ion channels are formed by symmetric homo-oligomers. In this study, we have proposed a hierarchical docking algorithm to predict the structure of C n symmetric protein complexes, which is referred to as CHDOCK. The symmetric binding modes were first constructed by an FFT-based docking algorithm and then optimized by our iterative scoring function for protein–protein interactions. When tested on a symmetric protein docking benchmark of 212 homo-oligomeric complexes with C n symmetry, CHDOCK obtained a significantly better performance in binding mode predictions than three state-of-the-art symmetric docking methods, M-ZDOCK, SAM, and SymmDock. When the top 10 predictions were considered, CHDOCK achieved a success rate of 44.81% and 72.17% for unbound docking and bound docking, respectively in comparison to those of 36.79% and 65.09% for M-ZDOCK, 31.60% and 54.25% for SAM, and 30.66% and 31.60% for SymmDock. CHDOCK is computationally efficient and can normally complete a symmetric docking calculation within 30 min. The CHDOCK can be freely accessed by a web server athttp://huanglab.phys.hust.edu.cn/hsymdock/.

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Biophysics Reports
Pages 65-72
Cite this article:
Yan Y, Huang S-Y. CHDOCK: a hierarchical docking approach for modeling C n symmetric homo-oligomeric complexes. Biophysics Reports, 2019, 5(2): 65-72. https://doi.org/10.1007/s41048-019-0088-0

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Received: 10 October 2018
Accepted: 20 December 2018
Published: 29 April 2019
© The Author(s) 2019

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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