Literature DB >> 18428873

Molecular modeling of nucleic acid structure.

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

Abstract

This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

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Year:  2001        PMID: 18428873      PMCID: PMC4029499          DOI: 10.1002/0471142700.nc0705s06

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


  28 in total

1.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

Authors:  Xiang-Jun Lu; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

2.  RNA conformational classes.

Authors:  Bohdan Schneider; Zdenek Morávek; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2004-03-11       Impact factor: 16.971

Review 3.  Modeling nucleic acids.

Authors:  Adelene Y L Sim; Peter Minary; Michael Levitt
Journal:  Curr Opin Struct Biol       Date:  2012-04-25       Impact factor: 6.809

4.  Conformations of the sugar-phosphate backbone in helical DNA crystal structures.

Authors:  B Schneider; S Neidle; H M Berman
Journal:  Biopolymers       Date:  1997       Impact factor: 2.505

Review 5.  Simulating DNA at low resolution.

Authors:  W K Olson
Journal:  Curr Opin Struct Biol       Date:  1996-04       Impact factor: 6.809

6.  Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.

Authors:  C Altona; M Sundaralingam
Journal:  J Am Chem Soc       Date:  1972-11-15       Impact factor: 15.419

7.  Measuring the geometry of DNA grooves.

Authors:  E Stofer; R Lavery
Journal:  Biopolymers       Date:  1994-03       Impact factor: 2.505

8.  The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

Authors:  M A el Hassan; C R Calladine
Journal:  J Mol Biol       Date:  1995-09-01       Impact factor: 5.469

9.  Mechanics of sequence-dependent stacking of bases in B-DNA.

Authors:  C R Calladine
Journal:  J Mol Biol       Date:  1982-10-25       Impact factor: 5.469

10.  Open Babel: An open chemical toolbox.

Authors:  Noel M O'Boyle; Michael Banck; Craig A James; Chris Morley; Tim Vandermeersch; Geoffrey R Hutchison
Journal:  J Cheminform       Date:  2011-10-07       Impact factor: 5.514

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  2 in total

Review 1.  Molecular modeling of nucleic acid structure.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-11

Review 2.  Molecular modeling of nucleic acid structure.

Authors:  Rodrigo Galindo-Murillo; Christina Bergonzo; Thomas E Cheatham
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2013-10-08
  2 in total

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