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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8265093 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT poppletonerik oxdnaorgapublicwebserverforcoarsegrainedsimulationsofdnaandrnananostructures AT romeroroger oxdnaorgapublicwebserverforcoarsegrainedsimulationsofdnaandrnananostructures AT mallyaaatmik oxdnaorgapublicwebserverforcoarsegrainedsimulationsofdnaandrnananostructures AT rovigattilorenzo oxdnaorgapublicwebserverforcoarsegrainedsimulationsofdnaandrnananostructures AT sulcpetr oxdnaorgapublicwebserverforcoarsegrainedsimulationsofdnaandrnananostructures |