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Darrin M. York, Ph.D.

Affiliations:

Rutgers University, New Brunswick, New Brunswick, NJ, United States

Area:

Theoretical Chemistry

Website:

http://theory.rutgers.edu/~york/

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Parents

Lee 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

George 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

Collaborators

BETA: Related publications

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

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