Additive CHARMM force field for naturally occurring modified ribonucleotides

Robustness in the fitting of molecular mechanics parameters

(2015) Kenno Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

(2014) Indrajit Deb et al.   BIOPOLYMERS

Significance of Molecular Dynamics Simulations for Life Sciences

(2014) Martin Karplus et al.   ISRAEL JOURNAL OF CHEMISTRY

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

(2014) Indrajit Deb et al.   Journal of Chemical Information and Modeling

Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics

(2014) Xiaoju Zhang et al.   Journal of Chemical Theory and Computation

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Backbone–Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure

(2013) Rachel N. Witts et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

(2013) G. A. Hudson et al.   RNA

Molecular structure and vibrational spectra of N4-acetylcytosine

(2013) Dapeng Zhou et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Structure and Function of Noncanonical Nucleobases

(2012) Thomas Carell et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

(2012) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

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

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

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

(2011) T Martin Schmeing et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome

(2011) O. Allner et al.   RNA

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

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

(2010) Nak-Kyoon Kim et al.   NUCLEIC ACIDS RESEARCH

The RNA modification database, RNAMDB: 2011 update

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

CHARMM: The biomolecular simulation program

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

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

(2008) Paul F Agris   EMBO REPORTS

Additive empirical force field for hexopyranose monosaccharides

(2008) Olgun Guvench et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

(2008) Lennart Nilsson   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effect of a Water Molecule on the Sugar Puckering of Uridine, 2‘-Deoxyuridine, and 2‘-O-Methyl Uridine Inserted in Duplexes

(2008) Sophie Barbe et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives

(2007) Yu-Cheng Chang et al.   BIOORGANIC & MEDICINAL CHEMISTRY