RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources
Abstract Background RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger structural changes or functions. Thus, it is essential to explore and visualize the RNA pocket to elucidate the structural and recognition mech...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04349-4 |
| _version_ | 1818591957206695936 |
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| author | Ting Zhou Huiwen Wang Chen Zeng Yunjie Zhao |
| author_facet | Ting Zhou Huiwen Wang Chen Zeng Yunjie Zhao |
| author_sort | Ting Zhou |
| collection | DOAJ |
| description | Abstract Background RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger structural changes or functions. Thus, it is essential to explore and visualize the RNA pocket to elucidate the structural and recognition mechanism for the RNA-ligand complex formation. Results In this work, we developed one user-friendly bioinformatics tool, RPocket. This database provides geometrical size, centroid, shape, secondary structure element for RNA pocket, RNA-ligand interaction information, and functional sites. We extracted 240 RNA pockets from 94 non-redundant RNA-ligand complex structures. We developed RPDescriptor to calculate the pocket geometrical property quantitatively. The geometrical information was then subjected to RNA-ligand binding analysis by incorporating the sequence, secondary structure, and geometrical combinations. This new approach takes advantage of both the atom-level precision of the structure and the nucleotide-level tertiary interactions. The results show that the higher-level topological pattern indeed improves the tertiary structure prediction. We also proposed a potential mechanism for RNA-ligand complex formation. The electrostatic interactions are responsible for long-range recognition, while the Van der Waals and hydrophobic contacts for short-range binding and optimization. These interaction pairs can be considered as distance constraints to guide complex structural modeling and drug design. Conclusion RPocket database would facilitate RNA-ligand engineering to regulate the complex formation for biological or medical applications. RPocket is available at http://zhaoserver.com.cn/RPocket/RPocket.html . |
| first_indexed | 2024-12-16T10:20:41Z |
| format | Article |
| id | doaj.art-3400070e02414f7e9dd97deb4f93a5f3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-16T10:20:41Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3400070e02414f7e9dd97deb4f93a5f32022-12-21T22:35:19ZengBMCBMC Bioinformatics1471-21052021-09-0122111610.1186/s12859-021-04349-4RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resourcesTing Zhou0Huiwen Wang1Chen Zeng2Yunjie Zhao3Department of Physics, Institute of Biophysics, Central China Normal UniversityDepartment of Physics, Institute of Biophysics, Central China Normal UniversityDepartment of Physics, George Washington UniversityDepartment of Physics, Institute of Biophysics, Central China Normal UniversityAbstract Background RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger structural changes or functions. Thus, it is essential to explore and visualize the RNA pocket to elucidate the structural and recognition mechanism for the RNA-ligand complex formation. Results In this work, we developed one user-friendly bioinformatics tool, RPocket. This database provides geometrical size, centroid, shape, secondary structure element for RNA pocket, RNA-ligand interaction information, and functional sites. We extracted 240 RNA pockets from 94 non-redundant RNA-ligand complex structures. We developed RPDescriptor to calculate the pocket geometrical property quantitatively. The geometrical information was then subjected to RNA-ligand binding analysis by incorporating the sequence, secondary structure, and geometrical combinations. This new approach takes advantage of both the atom-level precision of the structure and the nucleotide-level tertiary interactions. The results show that the higher-level topological pattern indeed improves the tertiary structure prediction. We also proposed a potential mechanism for RNA-ligand complex formation. The electrostatic interactions are responsible for long-range recognition, while the Van der Waals and hydrophobic contacts for short-range binding and optimization. These interaction pairs can be considered as distance constraints to guide complex structural modeling and drug design. Conclusion RPocket database would facilitate RNA-ligand engineering to regulate the complex formation for biological or medical applications. RPocket is available at http://zhaoserver.com.cn/RPocket/RPocket.html .https://doi.org/10.1186/s12859-021-04349-4Pocket databaseRNA-ligand interactionStructure predictionDrug discovery |
| spellingShingle | Ting Zhou Huiwen Wang Chen Zeng Yunjie Zhao RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources BMC Bioinformatics Pocket database RNA-ligand interaction Structure prediction Drug discovery |
| title | RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
| title_full | RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
| title_fullStr | RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
| title_full_unstemmed | RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
| title_short | RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
| title_sort | rpocket an intuitive database of rna pocket topology information with rna ligand data resources |
| topic | Pocket database RNA-ligand interaction Structure prediction Drug discovery |
| url | https://doi.org/10.1186/s12859-021-04349-4 |
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