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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/
Google:
"Darrin York"
Mean distance: 7.81
 
SNBCP

Parents

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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

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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
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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
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