Literature DB >> 18428877

Molecular modeling of nucleic acid structure: electrostatics and solvation.

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

Abstract

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics.

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Year:  2001        PMID: 18428877      PMCID: PMC4091950          DOI: 10.1002/0471142700.nc0709s05

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


  105 in total

Review 1.  Molecular dynamics simulation of nucleic acids.

Authors:  T E Cheatham; P A Kollman
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

2.  Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor.

Authors:  R L Williams; J Vila; G Perrot; H A Scheraga
Journal:  Proteins       Date:  1992-09

3.  An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

Authors:  Michael S Lee; Freddie R Salsbury; Mark A Olson
Journal:  J Comput Chem       Date:  2004-12       Impact factor: 3.376

4.  pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.

Authors:  D Bashford; M Karplus
Journal:  Biochemistry       Date:  1990-11-06       Impact factor: 3.162

5.  Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.

Authors:  Mika A Kastenholz; Philippe H Hünenberger
Journal:  J Chem Phys       Date:  2006-06-14       Impact factor: 3.488

6.  An accurate and simple quantum model for liquid water.

Authors:  Francesco Paesani; Wei Zhang; David A Case; Thomas E Cheatham; Gregory A Voth
Journal:  J Chem Phys       Date:  2006-11-14       Impact factor: 3.488

7.  Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.

Authors:  Asim Okur; Lauren Wickstrom; Melinda Layten; Raphäel Geney; Kun Song; Viktor Hornak; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2006-03       Impact factor: 6.006

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

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  1 in total

Review 1.  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

  1 in total

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