Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”

Frontiers in Molecular Dynamics Simulations of DNA

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

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

Monovalent Cation Size and DNA Conformational Stability

(2011) Earle Stellwagen et al.   BIOCHEMISTRY

Electrostatic Braiding and Homologous Pairing of DNA Double Helices

(2011) Ruggero Cortini et al.   BIOPHYSICAL JOURNAL

Solvent effects on the conformation of DNA dodecamer segment: A simulation study

(2011) X. Shen et al.   JOURNAL OF CHEMICAL PHYSICS

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Sequence-Specific Mg2+–DNA Interactions: A Molecular Dynamics Simulation Study

(2011) Weifeng Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA

(2011) Radovan Fiala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Do monovalent mobile ions affect DNA's flexibility at high salt content?

(2011) Alexey Savelyev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations

(2010) Roman Reshetnikov et al.   Journal of Chemical Theory and Computation

Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength

(2010) Chao Zhang et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns

(2010) Aymeric Naômé et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

(2010) Christopher M. Baker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Chemically accurate coarse graining of double-stranded DNA

(2010) A. Savelyev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic coarse-graining of molecular models by the Newton inversion method

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials

(2009) Robert C. DeMille et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

(2009) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

The impact of monovalent ion force field model in nucleic acids simulations

(2009) Agnes Noy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent-Induced DNA Conformational Transition

(2008) B. Gu et al.   PHYSICAL REVIEW LETTERS

Counterion-mediated electrostatic interactions between helical molecules

(2008) M. Kanduč et al.   Soft Matter