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OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures

OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics si...

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Detalles Bibliográficos
Autores principales: Poppleton, Erik, Romero, Roger, Mallya, Aatmik, Rovigatti, Lorenzo, Šulc, Petr
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8265093/
https://www.ncbi.nlm.nih.gov/pubmed/34009383
http://dx.doi.org/10.1093/nar/gkab324
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author Poppleton, Erik
Romero, Roger
Mallya, Aatmik
Rovigatti, Lorenzo
Šulc, Petr
author_facet Poppleton, Erik
Romero, Roger
Mallya, Aatmik
Rovigatti, Lorenzo
Šulc, Petr
author_sort Poppleton, Erik
collection PubMed
description OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user’s specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org.
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spelling pubmed-82650932021-07-09 OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures Poppleton, Erik Romero, Roger Mallya, Aatmik Rovigatti, Lorenzo Šulc, Petr Nucleic Acids Res Web Server Issue OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user’s specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org. Oxford University Press 2021-05-01 /pmc/articles/PMC8265093/ /pubmed/34009383 http://dx.doi.org/10.1093/nar/gkab324 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://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/ (https://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
Poppleton, Erik
Romero, Roger
Mallya, Aatmik
Rovigatti, Lorenzo
Šulc, Petr
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title_full OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title_fullStr OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title_full_unstemmed OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title_short OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
title_sort oxdna.org: a public webserver for coarse-grained simulations of dna and rna nanostructures
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8265093/
https://www.ncbi.nlm.nih.gov/pubmed/34009383
http://dx.doi.org/10.1093/nar/gkab324
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