Cargando…
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DN...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602492/ https://www.ncbi.nlm.nih.gov/pubmed/31114906 http://dx.doi.org/10.1093/nar/gkz412 |
_version_ | 1783431388377120768 |
---|---|
author | He, Jiahua Wang, Jun Tao, Huanyu Xiao, Yi Huang, Sheng-You |
author_facet | He, Jiahua Wang, Jun Tao, Huanyu Xiao, Yi Huang, Sheng-You |
author_sort | He, Jiahua |
collection | PubMed |
description | Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA–RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)–nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA–RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA–RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http://huanglab.phys.hust.edu.cn/hnadock/. |
format | Online Article Text |
id | pubmed-6602492 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66024922019-07-05 HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures He, Jiahua Wang, Jun Tao, Huanyu Xiao, Yi Huang, Sheng-You Nucleic Acids Res Web Server Issue Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA–RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)–nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA–RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA–RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http://huanglab.phys.hust.edu.cn/hnadock/. Oxford University Press 2019-07-02 2019-05-22 /pmc/articles/PMC6602492/ /pubmed/31114906 http://dx.doi.org/10.1093/nar/gkz412 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue He, Jiahua Wang, Jun Tao, Huanyu Xiao, Yi Huang, Sheng-You HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title | HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title_full | HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title_fullStr | HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title_full_unstemmed | HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title_short | HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures |
title_sort | hnadock: a nucleic acid docking server for modeling rna/dna–rna/dna 3d complex structures |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602492/ https://www.ncbi.nlm.nih.gov/pubmed/31114906 http://dx.doi.org/10.1093/nar/gkz412 |
work_keys_str_mv | AT hejiahua hnadockanucleicaciddockingserverformodelingrnadnarnadna3dcomplexstructures AT wangjun hnadockanucleicaciddockingserverformodelingrnadnarnadna3dcomplexstructures AT taohuanyu hnadockanucleicaciddockingserverformodelingrnadnarnadna3dcomplexstructures AT xiaoyi hnadockanucleicaciddockingserverformodelingrnadnarnadna3dcomplexstructures AT huangshengyou hnadockanucleicaciddockingserverformodelingrnadnarnadna3dcomplexstructures |