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RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources
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 fo...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8424408/ https://www.ncbi.nlm.nih.gov/pubmed/34496744 http://dx.doi.org/10.1186/s12859-021-04349-4 |
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author | Zhou, Ting Wang, Huiwen Zeng, Chen Zhao, Yunjie |
author_facet | Zhou, Ting Wang, Huiwen Zeng, Chen Zhao, Yunjie |
author_sort | Zhou, Ting |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04349-4. |
format | Online Article Text |
id | pubmed-8424408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-84244082021-09-08 RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources Zhou, Ting Wang, Huiwen Zeng, Chen Zhao, Yunjie BMC Bioinformatics Database 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04349-4. BioMed Central 2021-09-08 /pmc/articles/PMC8424408/ /pubmed/34496744 http://dx.doi.org/10.1186/s12859-021-04349-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Database Zhou, Ting Wang, Huiwen Zeng, Chen Zhao, Yunjie RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources |
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 | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8424408/ https://www.ncbi.nlm.nih.gov/pubmed/34496744 http://dx.doi.org/10.1186/s12859-021-04349-4 |
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