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Symmetric proteins play important roles in many biological processes, such as signal transduction and molecular transportation. Therefore, determining the symmetric oligomeric structure of subunits is crucial to investigate the molecular mechanism of the related processes. Due to the high cost and technical difficulties associated with many experimental methods, computational approaches, such as molecular docking, have played an important complementary role in the determination of symmetric complex structures, in which a benchmark data set is pressingly needed. In the present work, we develop a comprehensive and non-redundant benchmark for symmetric protein docking based on the structures in the Protein Data Bank (PDB). The diverse dataset consists of 251 targets, including 212 cases with cyclic groups symmetry, 35 cases with dihedral groups symmetry, 3 cases with cubic groups symmetry, and 1 case with helical symmetry. According to the conformational changes in the interface between bound and unbound structures, the 251 targets were classified into three groups: 176 "easy", 37 "medium", and 38 "difficult" cases. A preliminary docking test on the targets of cyclic groups symmetry with M-ZDOCK indicated that symmetric multimer docking remains challenging. The benchmark will be beneficial for the development of symmetric protein docking algorithms. The proposed benchmark data set is available for download at http://huanglab.phys.hust.edu.cn/SDBenchmark/.


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A Non-Redundant Benchmark for Symmetric Protein Docking

Show Author's information Yumeng YanSheng-You Huang( )
Institute of Biophysics, Huazhong University of Science and Technology, Wuhan 430074, China.

Abstract

Symmetric proteins play important roles in many biological processes, such as signal transduction and molecular transportation. Therefore, determining the symmetric oligomeric structure of subunits is crucial to investigate the molecular mechanism of the related processes. Due to the high cost and technical difficulties associated with many experimental methods, computational approaches, such as molecular docking, have played an important complementary role in the determination of symmetric complex structures, in which a benchmark data set is pressingly needed. In the present work, we develop a comprehensive and non-redundant benchmark for symmetric protein docking based on the structures in the Protein Data Bank (PDB). The diverse dataset consists of 251 targets, including 212 cases with cyclic groups symmetry, 35 cases with dihedral groups symmetry, 3 cases with cubic groups symmetry, and 1 case with helical symmetry. According to the conformational changes in the interface between bound and unbound structures, the 251 targets were classified into three groups: 176 "easy", 37 "medium", and 38 "difficult" cases. A preliminary docking test on the targets of cyclic groups symmetry with M-ZDOCK indicated that symmetric multimer docking remains challenging. The benchmark will be beneficial for the development of symmetric protein docking algorithms. The proposed benchmark data set is available for download at http://huanglab.phys.hust.edu.cn/SDBenchmark/.

Keywords:

benchmark, symmetric protein
Received: 14 July 2018 Accepted: 10 October 2018 Published: 14 May 2019 Issue date: June 2019
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Publication history

Received: 14 July 2018
Accepted: 10 October 2018
Published: 14 May 2019
Issue date: June 2019

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© The author(s) 2019

Acknowledgements

This work was supported by the National Key R&D Program of China (Nos. 2016YFC1305800 and 2016YFC1305805), the National Natural Science Foundation of China (No. 31670724), and the startup grant of Huazhong University of Science and Technology.

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