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Resource Type

  1. Software


  1. Resource Description
    August 2010 UPDATE New Releases (1.0) of NAST and C2A are available! Lots of exciting new features, detailed in the new manual NastTutorial.v4.pdf (under the "Downloads" button on the left). C2A has been separated from NAST, please download and install separately from the C2A project page: simtk.org/home/c2a. ***** Feb 2010 UPDATE 2 - If you are running C2A on a molecules that contains an "end" piece of length 1, please see the wiki for special instructions for fixing a bug that affects you ***** ***** Feb 2010 UPDATE 1 - Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki ***** ***** Nov 09 UPDATE - NAST is now available on most unix/pc/mac platforms. Please read the instructions posted on the wiki for details. ***** NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. TO USE NAST: Please read the README file under the downloads section. Keywords: Coarse grained, Knowledge-based, RNA
  2. Additional Name
    The Nucleic Acid Simulation Tool
  3. Contact
    Altman, Russ, M.D., Ph.D.
  4. Contact
    Jonikas, Magdalena
  5. Contact
    Laederach, Alain
  6. Contact
    Radmer, Randy
  7. Used by
    Stanford University
  8. Operating System
  9. Operating System
    Macintosh OS X
  10. Operating System
    Microsoft Windows
  11. Website(s)
Provenance Metadata About This Resource Record

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