Literature DB >> 24510799

Molecular modeling of nucleic acid structure.

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

Abstract

This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. The unit provides an overview of the computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, the generation of an initial model, and characterization of the overall three-dimensional structure.
Copyright © 2013 John Wiley & Sons, Inc.

Entities:  

Keywords:  experimental determination of structure; folding and conformational change; nucleic acid chemistry; nucleic acid structure and folding; structural analysis of biomolecules

Mesh:

Substances:

Year:  2013        PMID: 24510799      PMCID: PMC8830746          DOI: 10.1002/0471142700.nc0705s54

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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  1 in total

1.  Determinants of Oligonucleotide Selectivity of APOBEC3B.

Authors:  Jeffrey R Wagner; Özlem Demir; Michael A Carpenter; Hideki Aihara; Daniel A Harki; Reuben S Harris; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2018-09-10       Impact factor: 4.956

  1 in total

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