York DM - Search Results

1

CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. Brooks BR, et al. Among authors: york dm. J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. J Comput Chem. 2009. PMID: 19444816 Free PMC article. Review.

2

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.

Range K, Riccardi D, Cui Q, Elstner M, York DM. Range K, et al. Among authors: york dm. Phys Chem Chem Phys. 2005 Aug 21;7(16):3070-9. doi: 10.1039/b504941e. Epub 2005 Jul 7. Phys Chem Chem Phys. 2005. PMID: 16186912

3

Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction.

Major DT, York DM, Gao J. Major DT, et al. Among authors: york dm. J Am Chem Soc. 2005 Nov 30;127(47):16374-5. doi: 10.1021/ja055881u. J Am Chem Soc. 2005. PMID: 16305206

4

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems.

Lopez X, Dejaegere A, Leclerc F, York DM, Karplus M. Lopez X, et al. Among authors: york dm. J Phys Chem B. 2006 Jun 15;110(23):11525-39. doi: 10.1021/jp0603942. J Phys Chem B. 2006. PMID: 16771429

5

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.

Mayaan E, Moser A, MacKerell AD Jr, York DM. Mayaan E, et al. Among authors: york dm. J Comput Chem. 2007 Jan 30;28(2):495-507. doi: 10.1002/jcc.20474. J Comput Chem. 2007. PMID: 17186477 Free PMC article.

6

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.

Yang Y, Yu H, York D, Cui Q, Elstner M. Yang Y, et al. J Phys Chem A. 2007 Oct 25;111(42):10861-73. doi: 10.1021/jp074167r. Epub 2007 Oct 3. J Phys Chem A. 2007. PMID: 17914769

7

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.

Nam K, Gao J, York DM. Nam K, et al. Among authors: york dm. J Am Chem Soc. 2008 Apr 9;130(14):4680-91. doi: 10.1021/ja0759141. Epub 2008 Mar 18. J Am Chem Soc. 2008. PMID: 18345664 Free PMC article.

8

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

Nam K, Gao J, York DM. Nam K, et al. Among authors: york dm. RNA. 2008 Aug;14(8):1501-7. doi: 10.1261/rna.863108. Epub 2008 Jun 19. RNA. 2008. PMID: 18566190 Free PMC article.

9

Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models.

Wong KY, Xu Y, York DM. Wong KY, et al. Among authors: york dm. J Comput Chem. 2014 Jun 30;35(17):1302-16. doi: 10.1002/jcc.23628. Epub 2014 May 20. J Comput Chem. 2014. PMID: 24841935 Free PMC article.

10

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.

Panteva MT, Giambaşu GM, York DM. Panteva MT, et al. Among authors: york dm. J Comput Chem. 2015 May 15;36(13):970-82. doi: 10.1002/jcc.23881. Epub 2015 Mar 4. J Comput Chem. 2015. PMID: 25736394 Free PMC article.

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