All-atom polarizable force field for DNA based on the classical drude oscillator model

Polarizable Empirical Force Field for Acyclic Polyalcohols Based on the Classical Drude Oscillator

(2013) Xibing He et al.   BIOPOLYMERS

Six-site polarizable model of water based on the classical Drude oscillator

(2013) Wenbo Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

(2013) Arnošt Mládek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

(2012) Yun Luo et al.   FARADAY DISCUSSIONS

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

(2012) Tomáš Dršata et al.   Journal of Chemical Theory and Computation

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

Is DNA’s Rigidity Dominated by Electrostatic or Nonelectrostatic Interactions?

(2011) Alexey Savelyev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

(2011) Olivier Julien et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

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

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions

(2010) Christophe Oguey et al.   PLoS One

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

DNA curvature and flexibility in vitro and in vivo

(2010) Justin P. Peters et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

(2009) Christopher M. Baker et al.   JOURNAL OF MOLECULAR MODELING

Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, BI, and BIIForms of Duplex DNA

(2009) Alexander D. MacKerell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose

(2009) Elizabeth Hatcher et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsic flexibility of B-DNA: the experimental TRX scale

(2009) Brahim Heddi et al.   NUCLEIC ACIDS RESEARCH

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

(2009) Pedro E. M. Lopes et al.   THEORETICAL CHEMISTRY ACCOUNTS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator

(2008) Pedro E. M. Lopes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Importance of Accurate DNA Structures in Solution: The Jun–Fos Model

(2008) Brahim Heddi et al.   JOURNAL OF MOLECULAR BIOLOGY

Crystallographic Analysis of a Sex-Specific Enhancer Element: Sequence-Dependent DNA Structure, Hydration, and Dynamics

(2008) Narendra Narayana et al.   JOURNAL OF MOLECULAR BIOLOGY

Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field

(2008) Edward Harder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

31P NMR Investigation of Backbone Dynamics in DNA Binding Sites†

(2008) Ye Tian et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study

(2008) Elke Duchardt et al.   NUCLEIC ACIDS RESEARCH