Structure of the Singular Manifold of Protein Backbone and Its Applications
This paper aims to study the structure of the singular manifold of a fragment of protein backbone using the method of robot kinematics. By modeling chemical bonds as rigid links, and torsional motion around chemical bonds as revolute joints, a fragment of protein backbone turns into a kinematic link...
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| Format: | Article |
| Language: | English |
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IEEE
2020-01-01
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| Series: | IEEE Access |
| Subjects: | |
| Online Access: | https://ieeexplore.ieee.org/document/9025268/ |
| _version_ | 1811212123668217856 |
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| author | Yonggang Chen Guanfeng Liu Yong Yang |
| author_facet | Yonggang Chen Guanfeng Liu Yong Yang |
| author_sort | Yonggang Chen |
| collection | DOAJ |
| description | This paper aims to study the structure of the singular manifold of a fragment of protein backbone using the method of robot kinematics. By modeling chemical bonds as rigid links, and torsional motion around chemical bonds as revolute joints, a fragment of protein backbone turns into a kinematic linkage. The singular manifold of the forward kinematic map of this linkage contains important information about the structure of its inverse kinematics map, and the results also apply to the study of the conformation space of protein loops. By splitting the forward kinematic map into an orientation and position map, we derive equations of the singular manifolds for both maps and analyze their geometric and combinatorial structures. We discuss the application of singular manifolds in several problems of computational biology, including minimal parametrization of protein conformation space and conformation space sampling of protein loops. |
| first_indexed | 2024-04-12T05:23:30Z |
| format | Article |
| id | doaj.art-6a81c1d532c9462fa2a85dd967ef82db |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-04-12T05:23:30Z |
| publishDate | 2020-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-6a81c1d532c9462fa2a85dd967ef82db2022-12-22T03:46:22ZengIEEEIEEE Access2169-35362020-01-018484384845010.1109/ACCESS.2020.29785469025268Structure of the Singular Manifold of Protein Backbone and Its ApplicationsYonggang Chen0https://orcid.org/0000-0002-0970-6363Guanfeng Liu1Yong Yang2School of Electromechanical Engineering, Guangdong University of Technology, Guangdong, ChinaSchool of Electromechanical Engineering, Guangdong University of Technology, Guangdong, ChinaSchool of Mechatronics Engineering, Guangdong Polytechnic Normal University, Guangdong, ChinaThis paper aims to study the structure of the singular manifold of a fragment of protein backbone using the method of robot kinematics. By modeling chemical bonds as rigid links, and torsional motion around chemical bonds as revolute joints, a fragment of protein backbone turns into a kinematic linkage. The singular manifold of the forward kinematic map of this linkage contains important information about the structure of its inverse kinematics map, and the results also apply to the study of the conformation space of protein loops. By splitting the forward kinematic map into an orientation and position map, we derive equations of the singular manifolds for both maps and analyze their geometric and combinatorial structures. We discuss the application of singular manifolds in several problems of computational biology, including minimal parametrization of protein conformation space and conformation space sampling of protein loops.https://ieeexplore.ieee.org/document/9025268/Protein backboneforward and inverse kinematicssingular manifolddiscriminant curveprotein loop conformation space sampling |
| spellingShingle | Yonggang Chen Guanfeng Liu Yong Yang Structure of the Singular Manifold of Protein Backbone and Its Applications IEEE Access Protein backbone forward and inverse kinematics singular manifold discriminant curve protein loop conformation space sampling |
| title | Structure of the Singular Manifold of Protein Backbone and Its Applications |
| title_full | Structure of the Singular Manifold of Protein Backbone and Its Applications |
| title_fullStr | Structure of the Singular Manifold of Protein Backbone and Its Applications |
| title_full_unstemmed | Structure of the Singular Manifold of Protein Backbone and Its Applications |
| title_short | Structure of the Singular Manifold of Protein Backbone and Its Applications |
| title_sort | structure of the singular manifold of protein backbone and its applications |
| topic | Protein backbone forward and inverse kinematics singular manifold discriminant curve protein loop conformation space sampling |
| url | https://ieeexplore.ieee.org/document/9025268/ |
| work_keys_str_mv | AT yonggangchen structureofthesingularmanifoldofproteinbackboneanditsapplications AT guanfengliu structureofthesingularmanifoldofproteinbackboneanditsapplications AT yongyang structureofthesingularmanifoldofproteinbackboneanditsapplications |