Literature DB >> 18428876

Molecular modeling of nucleic acid structure: energy and sampling.

T E Cheatham1, B R Brooks, P A Kollman.   

Abstract

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT 7.5) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.

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Year:  2001        PMID： 18428876      PMCID： PMC4029503          DOI： 10.1002/0471142700.nc0708s04

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


  71 in total

1.  Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.

Authors:  Chia-En Chang; Michael K Gilson
Journal:  J Am Chem Soc       Date:  2004-10-13       Impact factor: 15.419

2.  Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs.

Authors:  Petr Sklenovský; Petra Florová; Pavel Banáš; Kamila Réblová; Filip Lankaš; Michal Otyepka; Jiří Šponer
Journal:  J Chem Theory Comput       Date:  2011-08-05       Impact factor: 6.006

3.  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

4.  Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.

Authors:  Tai-Sung Lee; Carlos Silva López; George M Giambasu; Monika Martick; William G Scott; Darrin M York
Journal:  J Am Chem Soc       Date:  2008-02-14       Impact factor: 15.419

5.  Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin.

Authors:  Angel E Garcia; Dietmar Paschek
Journal:  J Am Chem Soc       Date:  2007-12-23       Impact factor: 15.419

Review 6.  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

7.  Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

Authors:  Ramin M Abolfath; P K Biswas; R Rajnarayanam; Thomas Brabec; Reinhard Kodym; Lech Papiez
Journal:  J Phys Chem A       Date:  2012-04-05       Impact factor: 2.781

Review 8.  The ABCs of molecular dynamics simulations on B-DNA, circa 2012.

Authors:  David L Beveridge; Thomas E Cheatham; Mihaly Mezei
Journal:  J Biosci       Date:  2012-07       Impact factor: 1.826

9.  Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.

Authors:  Yang Yang; Haibo Yu; Darrin York; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

Review 10.  Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

Authors:  Pavel Banás; Petr Jurecka; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  Methods       Date:  2009-05-04       Impact factor: 3.608
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