Darrin M. York, Ph.D.
Affiliations: | Rutgers University, New Brunswick, New Brunswick, NJ, United States |
Area:
Theoretical ChemistryWebsite:
http://theory.rutgers.edu/~york/Google:
"Darrin York"Mean distance: 7.81 | S | N | B | C | P |
Parents
Sign in to add mentorLee G. Pedersen | grad student | 1993 | UNC Chapel Hill | |
(Molecular dynamics simulations of HIV-1 protease) | ||||
Weitao Yang | post-doc | 1993-1996 | Duke | |
(NSF postdoctoral fellow) | ||||
Martin Karplus | post-doc | 1997-1998 | Université Louis Pasteur, Strasbourg | |
(prior year PD @Harvard U) |
Children
Sign in to add traineeGeorge M. Giambasu | grad student | ||
Ming Huang | grad student | ||
Adam Moser | grad student | Loras College | |
Jinzhe Zeng | grad student | 2019- | Rutgers, New Brunswick |
Yang (Jana) Khandogin | grad student | 2003 | UMN |
Jana Shen | grad student | 1999-2003 | UMN |
Timothy J. Giese | grad student | 2005 | UMN |
Brent A. Gregersen | grad student | 2005 | UMN |
Evelyn A. Mayaan | grad student | 2005 | UMN |
Kevin Range | grad student | 1999-2005 | UMN |
George M. Giambasu | grad student | 2010 | UMN |
Haoyuan Chen | grad student | 2011-2016 | Rutgers, New Brunswick |
Kin-Yiu Wong | post-doc | 2010-2012 | Hong Kong Baptist University |
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Publications
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Giese TJ, Ekesan Ş, York DM. (2021) Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis. The Journal of Physical Chemistry. A |
Giese TJ, York DM. (2021) Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. Journal of Chemical Theory and Computation |
Lee TS, Allen BK, Giese TJ, et al. (2020) Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. Journal of Chemical Information and Modeling |
Lee TS, Lin Z, Allen BK, et al. (2020) Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials. Journal of Chemical Theory and Computation |
Tsai HC, Tao Y, Lee TS, et al. (2020) Validation of Free Energy Methods in AMBER. Journal of Chemical Information and Modeling |
He X, Liu S, Lee TS, et al. (2020) Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF. Acs Omega. 5: 4611-4619 |
Ganguly A, Weissman BP, Giese TJ, et al. (2020) Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nature Chemistry |
Ganguly A, Weissman BP, Piccirilli JA, et al. (2019) Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme. Acs Catalysis. 9: 10612-10617 |
Gaines CS, Piccirilli JA, York DM. (2019) The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. Rna (New York, N.Y.) |
Ekesan Ş, York DM. (2019) Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Research |