Difference between revisions of "External Resources"

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Here we provide a list of publicly available external resources that have been developed to help use oxDNA
 
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 [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package. This was developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [http://lammps.sandia.gov/doc/Section_packages.html#user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here].
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* The oxDNA and oxDNA2 models have been implemented in [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package. This was developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [http://lammps.sandia.gov/doc/Section_packages.html#user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here]. Accompanying paper: [http://dx.doi.org/10.1140/epje/i2018-11669-8 Eur. Phys. J. E]; [http://arxiv.org/abs/1802.07145 arXiv]
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* The tacoxDNA suite of tools allows the conversion of configurations to and from the oxDNA format. These can be used at the tacoxDNA [http://tacoxdna.sissa.it/ webserver] and the underlying python codes are available [https://github.com/lorenzo-rovigatti/tacoxDNA here]. Accopanying paper: [http://dx.doi.org/10.1002/jcc.26029 J. Comput. Chem.]
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* webDNA: a web front-end for oxDNA produced by the group of Matthew Patitz at University of Arkansa is available [https://github.com/uark-self-assembly here]
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* oxView: a browser-based viewer from the Šulc group is available [https://github.com/sulcgroup/oxdna-viewer here]. It is specifically designed for oxDNA, and allows manipulation as well as viewing of structures. Accompanying paper: [https://doi.org/10.1093/nar/gkaa417 Nucleic Acids Res.], [https://doi.org/10.1101/2020.01.24.917419 bioRxiv]
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* The Šulc group's oxDNA analysis tools: https://github.com/sulcgroup/oxdna_analysis_tools . Accompanying paper: [https://doi.org/10.1093/nar/gkaa417 Nucleic Acids Res.], [https://doi.org/10.1101/2020.01.24.917419 bioRxiv]
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* magicDNA: A design tool for complex origamis that uses oxDNA to aid iterative design is available [https://github.com/cmhuang2011/MagicDNA here]. Accompanying paper: [https://doi.org/10.1101/2020.05.28.119701 bioRxiv]
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* [http://oxDNA.org oxDNA.org]: This server is run by the Šulc group and allows users to run oxDNA simulations of large DNA nanostructures on GPUs.
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* An extension of the oxDNA/RNA models that allows proteins to be represented using an anisotropic network model has been developed by the Šulc group. The code and documentation are available [https://github.com/sulcgroup/anm-oxdna here]
  
 
or produce output in oxDNA format
 
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].  
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* 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]
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* [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].
  
 
If you have any resources that you want added do let us know.
 
If you have any resources that you want added do let us know.
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==Other DNA nanotechnology modelling tools==
 
==Other DNA nanotechnology modelling tools==
 
* [https://cando-dna-origami.org/ CanDo]
 
* [https://cando-dna-origami.org/ CanDo]
* multi-resolution DNA (mrDNA)
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* [http://bionano.physics.illinois.edu/dna-nanotechnology Aksimentiev group tools]
* NGR MD
 
  
 
==DNA nanotechnology design tools==
 
==DNA nanotechnology design tools==
 
* [https://cadnano.org/ cadnano]
 
* [https://cadnano.org/ cadnano]
 
* [http://yanlab.asu.edu/Resources.html Tiamat]
 
* [http://yanlab.asu.edu/Resources.html Tiamat]
* [http://www.vhelix.net/ vhelix]
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* [http://www.vhelix.net/ vHelix]
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* [http://bathebionano.org/software/ Wireframe DNA origami tools from the Bathe group]
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* [https://www.samson-connect.net/element/dda2a078-1ab6-96ba-0d14-ee1717632d7a.html Adenita]

Latest revision as of 16:29, 22 September 2020

Resources for oxDNA

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. Accompanying paper: Eur. Phys. J. E; arXiv
  • 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. Accopanying paper: J. Comput. Chem.
  • 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: Nucleic Acids Res., bioRxiv
  • magicDNA: A design tool for complex origamis that uses oxDNA to aid iterative design is available here. Accompanying paper: bioRxiv
  • oxDNA.org: This server is run by the Šulc group and allows users to run oxDNA simulations of large DNA nanostructures on GPUs.
  • An extension of the oxDNA/RNA models that allows proteins to be represented using an anisotropic network model has been developed by the Šulc group. The code and documentation are available here

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
  • Adenita A preprint introducing this design tool is available from bioRxiv.

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

Other DNA nanotechnology modelling tools

DNA nanotechnology design tools