The ABCs of molecular dynamics simulations on B-DNA, circa 2012

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

(2012) Surjit B Dixit et al.   JOURNAL OF BIOSCIENCES

Frontiers in Molecular Dynamics Simulations of DNA

(2011) Alberto Pérez et al.   ACCOUNTS OF CHEMICAL RESEARCH

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

(2011) C. Blanchet et al.   NUCLEIC ACIDS RESEARCH

The atomistic simulation of DNA

(2011) Charles A. Laughton et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions

(2010) Robert C. DeMille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A measure of bending in nucleic acids structures applied to A-tract DNA

(2010) F. Lankaš et al.   NUCLEIC ACIDS RESEARCH

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

(2009) Sobhan Sen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

(2009) F. Lankaš et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanism for the A-to-B Transition in DNA

(2008) Kelly M. Knee et al.   BIOPHYSICAL JOURNAL

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations

(2008) Poonam Singhal et al.   BIOPHYSICAL JOURNAL

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

(2008) Modesto Orozco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular dynamics simulations of nucleic acid–protein complexes

(2008) Alexander D MacKerell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

(2008) Daniel Svozil et al.   JOURNAL OF PHYSICAL CHEMISTRY B