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

Nucleic Acids Res. 2021 Jul 2;49(W1):W491-W498. doi: 10.1093/nar/gkab324.

Authors

Erik Poppleton¹, Roger Romero¹, Aatmik Mallya¹, Lorenzo Rovigatti², Petr Šulc¹

Affiliations

¹ School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA.
² Department of Physics, Sapienza Università di Roma, P.le A. Moro 2 00185, Rome, Italy.

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA / chemistry*
Internet
Molecular Dynamics Simulation*
Nanostructures / chemistry*
Nucleic Acid Conformation
RNA / chemistry*
Software*

Substances

RNA
DNA