Literature DB >> 24510800

Molecular modeling of nucleic acid structure: energy and sampling.

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

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.
Copyright © 2013 John Wiley & Sons, Inc.

Entities:  

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

Mesh：

Substances：

Year:  2013        PMID： 24510800      PMCID： PMC8843238          DOI： 10.1002/0471142700.nc0708s54

Source DB:  PubMed          Journal:  Curr Protoc Nucleic Acid Chem        ISSN： 1934-9270


  71 in total

Review 1.  Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results.

Authors:  D R Langley
Journal:  J Biomol Struct Dyn       Date:  1998-12

2.  Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

Authors:  Volodymyr Babin; Jason Baucom; Thomas A Darden; Celeste Sagui
Journal:  J Phys Chem B       Date:  2006-06-15       Impact factor: 2.991

3.  Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.

Authors:  Kwangho Nam; Jiali Gao; Darrin M York
Journal:  J Am Chem Soc       Date:  2008-03-18       Impact factor: 15.419

Review 4.  Nature and magnitude of aromatic stacking of nucleic acid bases.

Authors:  Jirí Sponer; Kevin E Riley; Pavel Hobza
Journal:  Phys Chem Chem Phys       Date:  2008-04-07       Impact factor: 3.676

5.  Chaos in protein dynamics.

Authors:  M Braxenthaler; R Unger; D Auerbach; J A Given; J Moult
Journal:  Proteins       Date:  1997-12

6.  Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

Authors:  Niel M Henriksen; Daniel R Roe; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2013-04-04       Impact factor: 2.991

7.  Polarization effects in molecular mechanical force fields.

Authors:  Piotr Cieplak; François-Yves Dupradeau; Yong Duan; Junmei Wang
Journal:  J Phys Condens Matter       Date:  2009-07-24       Impact factor: 2.333

8.  Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

Authors:  Gia G Maisuradze; Patrick Senet; Cezary Czaplewski; Adam Liwo; Harold A Scheraga
Journal:  J Phys Chem A       Date:  2010-04-08       Impact factor: 2.781

9.  Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.

Authors:  Tamar Schlick
Journal:  F1000 Biol Rep       Date:  2009-07-08

10.  Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.

Authors:  Marie Zgarbová; Michal Otyepka; Jiří Sponer; Arnošt Mládek; Pavel Banáš; Thomas E Cheatham; Petr Jurečka
Journal:  J Chem Theory Comput       Date:  2011-08-02       Impact factor: 6.006
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