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

Erik Poppleton; Roger Romero; Aatmik Mallya; Lorenzo Rovigatti; Petr Šulc

doi:10.1093/nar/gkab324

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

Erik Poppleton, Roger Romero, Aatmik Mallya, Lorenzo Rovigatti, Petr Šulc

Molecular Sciences, School of (SMS)

Research output: Contribution to journal › Article › peer-review

42 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	W491-W498
Journal	Nucleic acids research
Volume	49
Issue number	W1
DOIs	https://doi.org/10.1093/nar/gkab324
State	Published - Jul 2 2021

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkab324

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abstract = "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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OxDNA.org: A public webserver for coarse-grained simulations of DNA and RNA nanostructures

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