External Resources: Difference between revisions

Revision as of 07:35, 13 April 2020

Here we provide a list of publicly available external resources that have been developed to help use oxDNA

The oxDNA and oxDNA2 models have been implemented in LAMMPS in the USER-CGDNA package. This was developed by Oliver Henrich (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found here. The code comes with any regular download from the central LAMMPS repository, and it is also available here.

The tacoxDNA suite of tools allows the conversion of configurations to and from the oxDNA format. These can be used at the tacoxDNA webserver and the underlying python codes are available here.

webDNA: a web front-end for oxDNA produced by the group of Matthew Patitz at University of Arkansa is available here

oxView: a browser-based viewer from the Šulc group is available here. It is specifically designed for oxDNA, and allows manipulation as well as viewing of structures. Accompanying paper: bioRxiv

The Šulc group's oxDNA analysis tools: https://github.com/sulcgroup/oxdna_analysis_tools . Accompanying paper: bioRxiv

or produce output in oxDNA format

multi-resolution DNA (mrDNA). This programme from the Aksimentiev group can simulate DNA nanostructures at multiple coarser levels of detail than oxDNA. It can output in oxDNA format. A tutorial can be found here and the repository for the code here. Accompanying paper: Nucleic Acids Res.; bioRxiv

If you have any resources that you want added do let us know.

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 or produce output in oxDNA format
-* multi-resolution DNA (mrDNA). This programme from the [http://bionano.physics.illinois.edu/ Aksimentiev group] can simulate DNA nanostructures at multiple coarser levels of detail than oxDNA. It can output in oxDNA format. A tutorial can be found [http://www.ks.uiuc.edu/Training/Workshop/Urbana2018c/tutorials/multi-resolution-dna-nanotechnology.pdf here] and the repository for the code [https://gitlab.engr.illinois.edu/tbgl/tools/mrdna here]. Accompanying paper: [https://doi.org/10.1101/865733 bioRxiv]; [https://doi.org/10.1093/nar/gkaa200 Nucleic Acids Res.]
+* multi-resolution DNA (mrDNA). This programme from the [http://bionano.physics.illinois.edu/ Aksimentiev group] can simulate DNA nanostructures at multiple coarser levels of detail than oxDNA. It can output in oxDNA format. A tutorial can be found [http://www.ks.uiuc.edu/Training/Workshop/Urbana2018c/tutorials/multi-resolution-dna-nanotechnology.pdf here] and the repository for the code [https://gitlab.engr.illinois.edu/tbgl/tools/mrdna here]. Accompanying paper: [https://doi.org/10.1093/nar/gkaa200 Nucleic Acids Res.]; [https://doi.org/10.1101/865733 bioRxiv]
 * [https://www.samson-connect.net/element/dda2a078-1ab6-96ba-0d14-ee1717632d7a.html Adenita] A preprint introducing this design tool is available from [https://doi.org/10.1101/849976 bioRxiv].