TacoxDNA: A user-friendly web server for simulations of complex DNA structures,from single strands to origami |
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| Authors: | Antonio Suma Erik Poppleton Michael Matthies Petr Šulc Flavio Romano Ard A Louis Jonathan P K Doye Cristian Micheletti Lorenzo Rovigatti |
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| Institution: | 1. Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122;2. Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281;3. Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany;4. Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, Via Torino, 155, 30172 Venezia Mestre, Italy;5. Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP UK;6. Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ UK;7. SISSA—Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136 Trieste, Italy;8. Dipartimento di Fisica, Sapienza Universitá di Roma, Piazzale A. Moro, 2, 00185 Rome, Italy |
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| 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 . © 2019 Wiley Periodicals, Inc. |
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| Keywords: | “DNA input formats conversion” “XYZ centerline cadnano Tiamat CanDo and full atom conversion to oxDNA and full atom” “oxDNA webserver” ■ |
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