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Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features...

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Detalles Bibliográficos
Autores principales: Li, Shuxiang, Olson, Wilma K, Lu, Xiang-Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602438/
https://www.ncbi.nlm.nih.gov/pubmed/31114927
http://dx.doi.org/10.1093/nar/gkz394
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author Li, Shuxiang
Olson, Wilma K
Lu, Xiang-Jun
author_facet Li, Shuxiang
Olson, Wilma K
Lu, Xiang-Jun
author_sort Li, Shuxiang
collection PubMed
description Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double-helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double-helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org.
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spelling pubmed-66024382019-07-05 Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures Li, Shuxiang Olson, Wilma K Lu, Xiang-Jun Nucleic Acids Res Web Server Issue Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double-helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double-helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org. Oxford University Press 2019-07-02 2019-05-22 /pmc/articles/PMC6602438/ /pubmed/31114927 http://dx.doi.org/10.1093/nar/gkz394 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Li, Shuxiang
Olson, Wilma K
Lu, Xiang-Jun
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title_full Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title_fullStr Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title_full_unstemmed Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title_short Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
title_sort web 3dna 2.0 for the analysis, visualization, and modeling of 3d nucleic acid structures
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602438/
https://www.ncbi.nlm.nih.gov/pubmed/31114927
http://dx.doi.org/10.1093/nar/gkz394
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