TacoxDNA

A user-friendly web server for simulations of complex DNA structures, from single strands to origami

Antonio Suma, Erik Poppleton, Michael Matthies, Petr Sulc, Flavio Romano, Ard A. Louis, Jonathan P.K. Doye, Cristian Micheletti, Lorenzo Rovigatti

Research output: Contribution to journalArticle

Abstract

Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it.

Original languageEnglish (US)
JournalJournal of Computational Chemistry
DOIs
StatePublished - Jan 1 2019

Fingerprint

Web Server
Molecular Dynamics Simulation
DNA
Servers
Biophysics
Materials Science
Structural Model
Software Package
Open Source
Interoperability
Medicine
Knot
Nucleic acids
Simulation
Complement
Nucleic Acids
Molecular dynamics
Topology
Ring
Line

Keywords

  • cadnano
  • CanDo and full atom conversion to oxDNA and full atom”
  • Tiamat
  • “DNA input formats conversion”
  • “oxDNA webserver” ■
  • “XYZ centerline

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

TacoxDNA : A user-friendly web server for simulations of complex DNA structures, from single strands to origami. / Suma, Antonio; Poppleton, Erik; Matthies, Michael; Sulc, Petr; Romano, Flavio; Louis, Ard A.; Doye, Jonathan P.K.; Micheletti, Cristian; Rovigatti, Lorenzo.

In: Journal of Computational Chemistry, 01.01.2019.

Research output: Contribution to journalArticle

Suma, Antonio ; Poppleton, Erik ; Matthies, Michael ; Sulc, Petr ; Romano, Flavio ; Louis, Ard A. ; Doye, Jonathan P.K. ; Micheletti, Cristian ; Rovigatti, Lorenzo. / TacoxDNA : A user-friendly web server for simulations of complex DNA structures, from single strands to origami. In: Journal of Computational Chemistry. 2019.
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