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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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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Literature Cited

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Internet Resources
  Lists of available software.
  GAMESS Web site.‐state_physics_software
  GAMESS‐UK Web site.
  Gaussian program Web site.
  Jaguar Web site.
  MolPro Web site.
  Q‐chem Web site.
  Spartan Web site.
  ZINDO Web site.
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