Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

(2013) Jason D. Tubbs et al.   BIOCHEMISTRY

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models

(2012) Zhou Gong et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

(2011) Ilyas Yildirim 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

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

(2011) Ilyas Yildirim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

(2010) Ilyas Yildirim et al.   Journal of Chemical Theory and Computation

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin−Spin Couplings

(2009) Zuzana Vokáčová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Force field parameters for rotation around χ torsion axis in nucleic acids

(2008) Hirotaka Ode et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY