Darrin M. York

Exact Relation between Potential of Mean Force and Free-Energy Profile

J. Chem. Theory Comput., (2012) 8, 3998-4003
DOI: 10.1021/ct300392f Download PDF

Mapping l1 ligase ribozyme conformational switch

J. Mol. Biol., (2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035 Download PDF

Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

Angew. Chem. Int. Ed., (2012) 51, 647-651
DOI: 10.1002/anie.201104147 Download PDF

Density-functional expansion methods: Generalization of the auxiliary basis

J. Chem. Phys., (2011) 134, 194103
DOI: 10.1063/1.3587052 Download PDF

Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

DOI: 10.1021/ct100467t Download PDF

Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

J. Phys. Chem. Lett., (2011) 2, 2538-2543
DOI: 10.1021/jz201106y Download PDF

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts 

Nucleic Acids Res., (2011) 39, 3988-4006
DOI: 10.1093/nar/gkq1341 Download PDF

Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations

DOI: 10.1016/S1574-1400(10)06001-9 Download PDF

Exocyclic deoxyadenosine adducts of 1,2,3,4-Diepoxybutane: Synthesis, structural elucidation, and mechanistic studie

Chem. Res. Toxicol., (2010) 23, 118-133
DOI: 10.1021/tx900312e Download PDF

Computational mutagenesis studies of hammerhead ribozyme catalysis

J. Am. Chem. Soc., (2010) 132, 13505-13518
DOI: 10.1021/ja105956u Download PDF

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