Rutgers Main | CIRC | Quantitative Biology   

Darrin M. York

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

RNA, (2008) 14, 1501-1507
DOI: 10.1261/rna.863108 Download PDF

Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory. 1. Parameterization

J. Chem. Theory Comput., (2008) 4, 2067-2084
DOI: 10.1021/ct800330d Download PDF

Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables

J. Chem. Phys., (2008) 129, 016102
DOI: 10.1063/1.2945897 Download PDF

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

J. Comput. Chem., (2008) 29, 1895-1904
DOI: 10.1002/jcc.20946 Download PDF

Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

J. Am. Chem. Soc., (2008) 130, 4680-4691
DOI: 10.1021/ja0759141 Download PDF

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

J. Am. Chem. Soc., (2008) 130, 3053-3064
DOI: 10.1021/ja076529e Download PDF

Solvent structure and hammerhead ribozyme catalysis

Chem. Biol., (2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010 Download PDF

Contracted auxiliary Gaussian basis integral and derivative evaluation

J. Chem. Phys., (2008) 128, 064104
DOI: 10.1063/1.2821745 Download PDF

Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

J. Am. Chem. Soc., (2008) 130, 7168-7169
DOI: 10.1021/ja711242b Download PDF

Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

J. Chem. Theory Comput., (2007) 3, 325-327
DOI: 10.1021/ct6003142 Download PDF