Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

Christina Bergonzo1, Rodrigo Galindo‐Murillo1, Thomas E. Cheatham1

1 University of Utah, Salt Lake City, Utah
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.8
DOI:  10.1002/0471142700.nc0708s54
Online Posting Date:  October, 2013
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Abstract

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields. Curr. Protoc. Nucleic Acid Chem. 54:7.8.1‐7.8.21. © 2013 by John Wiley & Sons, Inc.

Keywords: nucleic acid chemistry; nucleic acid structure and folding; structural analysis of biomolecules; experimental determination of structure; molecular modeling; molecular dynamics; force fields

     
 
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Table of Contents

  • The Energy Representation
  • Beyond Energy Evaluation
  • Summary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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Internet Resources
  http://www.ccl.net
  Lists of available software.
  http://www.netsci.org/Resources/Software/Modeling
  GAMESS Web site.
  http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid‐state_physics_software
  GAMESS‐UK Web site.
  http://www.msg.ameslab.gov/GAMESS/GAMESS.html
  Gaussian program Web site.
  http://www.cfs.dl.ac.uk/
  Jaguar Web site.
  http://www.gaussian.com
  MolPro Web site.
  http://www.schrodinger.com
  NWChem.
  http://www.molpro.net
  Q‐chem Web site.
  http://www.nwchem‐sw.org/index.php/Main_Page
  Spartan Web site.
  http://www.q‐chem.com
  Terachem/Petachem.
   http://www.wavefun.com
  Turbomole.
  http://www.petachem.com/products.html
  ZINDO Web site.
  http://www.turbomole.com/
  http://www.msi.com
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