The intrinsic mechanics of B-DNA in solution characterized by NMR

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

(2015) K. Vanommeslaeghe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

(2015) Rodrigo Galindo-Murillo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout

(2014) Xiaoqian Xu et al.   BIOCHEMISTRY

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

(2014) Sabrina Harteis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNA Architecture, Deformability, and Nucleosome Positioning

(2014) Fei Xu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

(2014) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

(2013) Jana Přecechtělová 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

Probing Sequence-Specific DNA Flexibility in A-Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance 13C Relaxation and Molecular Dynamics Simulations

(2012) Evgenia N. Nikolova et al.   BIOCHEMISTRY

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

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

Working the kinks out of nucleosomal DNA

(2011) Wilma K Olson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

(2011) Tatsuya Maehigashi et al.   NUCLEIC ACIDS RESEARCH

Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations

(2010) Jana Přecechtělová et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2010) Christophe Oguey et al.   PLoS One

Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR

(2009) Evgenia N. Nikolova et al.   JOURNAL OF BIOMOLECULAR NMR

Sequence-Dependent DNA Flexibility Mediates DNase I Cleavage

(2009) Brahim Heddi et al.   JOURNAL OF MOLECULAR BIOLOGY

Intrinsic flexibility of B-DNA: the experimental TRX scale

(2009) Brahim Heddi et al.   NUCLEIC ACIDS RESEARCH

13C Relaxation Studies of the DNA Target Sequence forHhaI Methyltransferase Reveal Unique Motional Properties†

(2008) Zahra Shajani et al.   BIOCHEMISTRY

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

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

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

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

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

(2008) Markus Zweckstetter   Nature Protocols

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

(2008) Elke Duchardt et al.   NUCLEIC ACIDS RESEARCH

Towards a molecular dynamics consensus view of B-DNA flexibility

(2008) Alberto Pérez et al.   NUCLEIC ACIDS RESEARCH

Helical coherence of DNA in crystals and solution

(2008) Aaron Wynveen et al.   NUCLEIC ACIDS RESEARCH