Literature DB >> 10753816

Nucleic acids: theory and computer simulation, Y2K.

D L Beveridge1, K J McConnell.   

Abstract

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.

Entities:  

Mesh：

Substances：

Year:  2000        PMID： 10753816     DOI： 10.1016/s0959-440x(00)00076-2

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


  50 in total

1.  On the molecular discrimination between adenine and guanine by proteins.

Authors:  I Nobeli; R A Laskowski; W S Valdar; J M Thornton
Journal:  Nucleic Acids Res       Date:  2001-11-01       Impact factor: 16.971

2.  DNA polymorphism: a comparison of force fields for nucleic acids.

Authors:  Swarnalatha Y Reddy; Fabrice Leclerc; Martin Karplus
Journal:  Biophys J       Date:  2003-03       Impact factor: 4.033

3.  Hidden Markov models from molecular dynamics simulations on DNA.

Authors:  Kelly M Thayer; D L Beveridge
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-18       Impact factor: 11.205

4.  Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

Authors:  Lihua Wang; Brian E Hingerty; A R Srinivasan; Wilma K Olson; Suse Broyde
Journal:  Biophys J       Date:  2002-07       Impact factor: 4.033

5.  Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

Authors:  Kamila Réblová; Nad'a Spacková; Richard Stefl; Kristina Csaszar; Jaroslav Koca; Neocles B Leontis; Jirí Sponer
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

6.  Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies.

Authors:  Donald Hamelberg; Loren Dean Williams; W David Wilson
Journal:  Nucleic Acids Res       Date:  2002-08-15       Impact factor: 16.971

7.  Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe.

Authors:  Mark M Somoza; Daniele Andreatta; Catherine J Murphy; Robert S Coleman; Mark A Berg
Journal:  Nucleic Acids Res       Date:  2004-05-06       Impact factor: 16.971

8.  Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

Authors:  Manuel Rueda; Elena Cubero; Charles A Laughton; Modesto Orozco
Journal:  Biophys J       Date:  2004-08       Impact factor: 4.033

9.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.

Authors:  David L Beveridge; Gabriela Barreiro; K Suzie Byun; David A Case; Thomas E Cheatham; Surjit B Dixit; Emmanuel Giudice; Filip Lankas; Richard Lavery; John H Maddocks; Roman Osman; Eleanore Seibert; Heinz Sklenar; Gautier Stoll; Kelly M Thayer; Péter Varnai; Matthew A Young
Journal:  Biophys J       Date:  2004-08-23       Impact factor: 4.033

10.  Ion motions in molecular dynamics simulations on DNA.

Authors:  Sergei Y Ponomarev; Kelly M Thayer; David L Beveridge
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-01       Impact factor: 11.205
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.