Literature DB >> 18304803

Recent advances in the study of nucleic acid flexibility by molecular dynamics.

Modesto Orozco1, Agnes Noy, Alberto Pérez.   

Abstract

The recent use of molecular dynamics (MD) simulations to study flexibility of nucleic acids has been reviewed from an analysis of the publications appearing in the past two years (from 2005 till date). Despite the existence of some unsolved problems in the methodologies, these years have been witness to major advances in the field. Based on a critical review of the most recent contributions, excitement exists on the expected evolution of the field in the next years.

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Year:  2008        PMID: 18304803     DOI: 10.1016/j.sbi.2008.01.005

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  44 in total

1.  Evaluation of DNA Force Fields in Implicit Solvation.

Authors:  Thomas Gaillard; David A Case
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

2.  Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

Authors:  Surjit B Dixit; Mihaly Mezei; David L Beveridge
Journal:  J Biosci       Date:  2012-07       Impact factor: 1.826

3.  Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

Authors:  Vojtech Mlýnský; Pavel Banás; Daniel Hollas; Kamila Réblová; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

4.  Analysis of a DNA simulation model through hairpin melting experiments.

Authors:  Margaret C Linak; Kevin D Dorfman
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

5.  A mesoscale model of DNA and its renaturation.

Authors:  E J Sambriski; D C Schwartz; J J de Pablo
Journal:  Biophys J       Date:  2009-03-04       Impact factor: 4.033

Review 6.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

7.  Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations.

Authors:  Ranjit P Bahadur; Srinivasaraghavan Kannan; Martin Zacharias
Journal:  Biophys J       Date:  2009-12-16       Impact factor: 4.033

8.  Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations.

Authors:  Jeremy Curuksu; Jiri Sponer; Martin Zacharias
Journal:  Biophys J       Date:  2009-10-07       Impact factor: 4.033

9.  Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A{middle dot}A base pairing and a putative structure of the coralyne-induced homo-adenine duplex.

Authors:  In Suk Joung; Ozgül Persil Cetinkol; Nicholas V Hud; Thomas E Cheatham
Journal:  Nucleic Acids Res       Date:  2009-12       Impact factor: 16.971

10.  Conformational analysis of nucleic acids revisited: Curves+.

Authors:  R Lavery; M Moakher; J H Maddocks; D Petkeviciute; K Zakrzewska
Journal:  Nucleic Acids Res       Date:  2009-07-22       Impact factor: 16.971

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