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ORCIDDarrin M. York
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2020 – today
- 2021
[j16]Han Zhang
, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im:
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. J. Chem. Inf. Model. 61(9): 4145-4151 (2021)- 2020
- [j15]Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M. Merz Jr., Darrin M. York:
Validation of Free Energy Methods in AMBER. J. Chem. Inf. Model. 60(11): 5296-5300 (2020) - [j14]Tai-Sung Lee, Bryce K. Allen, Timothy J. Giese, Zhenyu Guo, Pengfei Li, Charles Lin, T. Dwight McGee, David A. Pearlman, Brian K. Radak, Yujun Tao, Hsu-Chun Tsai, Huafeng Xu, Woody Sherman, Darrin M. York:
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. J. Chem. Inf. Model. 60(11): 5595-5623 (2020)
2010 – 2019
- 2019
- [j13]Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.:
Using AMBER18 for Relative Free Energy Calculations. J. Chem. Inf. Model. 59(7): 3128-3135 (2019) - 2018
- [j12]Tai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian E. Roitberg, David A. Case, Ross C. Walker, Darrin M. York:
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J. Chem. Inf. Model. 58(10): 2043-2050 (2018) - 2016
- [j11]Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo:
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. J. Comput. Aided Mol. Des. 30(7): 533-539 (2016) - [c2]Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha:
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. ICPP 2016: 628-637 - [i1]Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha:
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. CoRR abs/1601.05439 (2016) - 2015
- [j10]Maria T. Panteva, George M. Giambasu, Darrin M. York:
Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations. J. Comput. Chem. 36(13): 970-982 (2015) - [j9]Ming Huang, Timothy J. Giese, Darrin M. York:
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models. J. Comput. Chem. 36(18): 1370-1389 (2015) - 2014
- [j8]Kin-Yiu Wong, Yuqing Xu, Darrin M. York:
Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J. Comput. Chem. 35(17): 1302-1316 (2014) - 2013
- [c1]Brian K. Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy, Shantenu Jha:
A framework for flexible and scalable replica-exchange on production distributed CI. XSEDE 2013: 26:1-26:8
2000 – 2009
- 2009
- [j7]Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, V. Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - 2008
- [j6]Timothy J. Giese, Darrin M. York:
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. J. Comput. Chem. 29(12): 1895-1904 (2008) - 2007
- [j5]Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York:
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J. Comput. Chem. 28(2): 495-507 (2007) - 2006
- [j4]Brent A. Gregersen, Darrin M. York:
A charge-scaling implementation of the variational electrostatic projection method. J. Comput. Chem. 27(1): 103-115 (2006) - 2003
- [j3]Edward C. Sherer, Darrin M. York, Christopher J. Cramer:
Fast approximate methods for calculating nucleic acid base pair interaction energies. J. Comput. Chem. 24(1): 57-67 (2003) - 2000
- [j2]Jana Khandogin, Anguang Hu, Darrin M. York:
Electronic structure properties of solvated biomolecules: A quantum approach for macromolecular characterization. J. Comput. Chem. 21(16): 1562-1571 (2000)
1990 – 1999
- 1994
- [j1]Darrin M. York, Lee J. Bartolotti, Thomas A. Darden, Lee G. Pedersen, M. W. Anderson:
Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc. J. Comput. Chem. 15(1): 61-71 (1994)
Coauthor Index
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