A Non-Redundant Benchmark for Symmetric Protein Docking
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 t...
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Tsinghua University Press
2019-06-01
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| Series: | Big Data Mining and Analytics |
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| Online Access: | https://www.sciopen.com/article/10.26599/BDMA.2018.9020035 |
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| author | Yumeng Yan Sheng-You Huang |
| author_facet | Yumeng Yan Sheng-You Huang |
| author_sort | Yumeng Yan |
| collection | DOAJ |
| description | 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/. |
| format | Article |
| id | doaj-art-ba758297450e4d759620b4e8d7fe450f |
| institution | Kabale University |
| issn | 2096-0654 |
| language | English |
| publishDate | 2019-06-01 |
| publisher | Tsinghua University Press |
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| series | Big Data Mining and Analytics |
| spelling | doaj-art-ba758297450e4d759620b4e8d7fe450f2025-02-02T03:44:40ZengTsinghua University PressBig Data Mining and Analytics2096-06542019-06-0122929910.26599/BDMA.2018.9020035A Non-Redundant Benchmark for Symmetric Protein DockingYumeng Yan0Sheng-You Huang1<institution content-type="dept">Institute of Biophysics</institution>, <institution>Huazhong University of Science and Technology</institution>, <city>Wuhan</city> <postal-code>430074</postal-code>, <country>China</country>.<institution content-type="dept">Institute of Biophysics</institution>, <institution>Huazhong University of Science and Technology</institution>, <city>Wuhan</city> <postal-code>430074</postal-code>, <country>China</country>.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/.https://www.sciopen.com/article/10.26599/BDMA.2018.9020035benchmarksymmetric protein |
| spellingShingle | Yumeng Yan Sheng-You Huang A Non-Redundant Benchmark for Symmetric Protein Docking Big Data Mining and Analytics benchmark symmetric protein |
| title | A Non-Redundant Benchmark for Symmetric Protein Docking |
| title_full | A Non-Redundant Benchmark for Symmetric Protein Docking |
| title_fullStr | A Non-Redundant Benchmark for Symmetric Protein Docking |
| title_full_unstemmed | A Non-Redundant Benchmark for Symmetric Protein Docking |
| title_short | A Non-Redundant Benchmark for Symmetric Protein Docking |
| title_sort | non redundant benchmark for symmetric protein docking |
| topic | benchmark symmetric protein |
| url | https://www.sciopen.com/article/10.26599/BDMA.2018.9020035 |
| work_keys_str_mv | AT yumengyan anonredundantbenchmarkforsymmetricproteindocking AT shengyouhuang anonredundantbenchmarkforsymmetricproteindocking AT yumengyan nonredundantbenchmarkforsymmetricproteindocking AT shengyouhuang nonredundantbenchmarkforsymmetricproteindocking |