Parmbsc1: a refined force field for DNA simulations

All-atom crystal simulations of DNA and RNA duplexes

(2015) Chunmei Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

MD and NMR Analyses of Choline and TMA Binding to Duplex DNA: On the Origins of Aberrant Sequence-Dependent Stability by Alkyl Cations in Aqueous and Water-Free Solvents

(2014) Guillem Portella et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Direct measurement of the dielectric polarization properties of DNA

(2014) A. Cuervo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the absence of intrahelical DNA dynamics on the μs to ms timescale

(2014) Rodrigo Galindo-Murillo et al.   Nature Communications

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

Dramatic Effect of Furanose C2′ Substitution on Structure and Stability: Directing the Folding of the Human Telomeric Quadruplex with a Single Fluorine Atom

(2013) Nerea Martín-Pintado et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NAFlex: a web server for the study of nucleic acid flexibility

(2013) Adam Hospital et al.   NUCLEIC ACIDS RESEARCH

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

(2012) Adam Hospital et al.   BIOINFORMATICS

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

Exploring polymorphisms in B-DNA helical conformations

(2012) Pablo D. Dans et al.   NUCLEIC ACIDS RESEARCH

Length Scale Dependence of DNA Mechanical Properties

(2012) Agnes Noy et al.   PHYSICAL REVIEW LETTERS

Frontiers in Molecular Dynamics Simulations of DNA

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

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

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies

(2010) Ignacio Soteras et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies†

(2009) Ignacio Soteras et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

(2009) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

How stiff is DNA?

(2009) Guohui Zheng et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

NMR: prediction of molecular alignment from structure using the PALES software

(2008) Markus Zweckstetter   Nature Protocols

Towards a molecular dynamics consensus view of B-DNA flexibility

(2008) Alberto Pérez et al.   NUCLEIC ACIDS RESEARCH