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New Publications

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

Contracted auxiliary Gaussian basis integral and derivative evaluation

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

Solvent structure and hammerhead ribozyme catalysis

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

New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution

DOI: 10.1002/9780470191675.ch12 Download PDF

Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

J. Chem. Phys., (2007) 127, 194101
DOI: 10.1063/1.2778428 Download PDF

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

J. Phys Chem. A, (2007) 111, 10861-10873
DOI: 10.1021/jp074167r 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

Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

J. Chem. Theory Comput., (2007) 3, 486-504
DOI: 10.1021/ct6002466 Download PDF

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