Unit

UNIT 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

  1. Rodrigo Galindo-Murillo,
  2. Christina Bergonzo,
  3. Thomas E. Cheatham III

Published Online: 26 MAR 2014

DOI: 10.1002/0471142700.nc0710s56

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Galindo-Murillo, R., Bergonzo, C. and Cheatham, T. E. 2014. Molecular Modeling of Nucleic Acid Structure: Setup and Analysis. Current Protocols in Nucleic Acid Chemistry. 7:7.10:7.10.1–7.10.21.

Author Information

  1. Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah

Publication History

  1. Published Online: 26 MAR 2014

Abstract

The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. The unit describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories. Curr. Protoc. Nucleic Acid Chem. 56:7.10.1-7.10.21. © 2014 by John Wiley & Sons, Inc.

Keywords:

  • nucleic acid chemistry;
  • nucleic acid structure and folding;
  • force field review;
  • simulation setup and analysis;
  • simulation protocols;
  • sampling methods