Darrin M. York

27 papers B 1Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.
J. Chem. Inf. Model.
Hsu-Chun Tsai, Shi Zhang, Tai-Sung Lee, Timothy J. Giese, Charles Lin, James Xu, Yinhui Yi, Darrin M. York, Abir Ganguly, Albert C. Pan
2026 J jnl
Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization.
J. Chem. Inf. Model.
Alejandro Blanco-Gonzalez, William Betancourt, Ryan Snyder, Shi Zhang, Timothy J. Giese, Zeke Piskulich, Andreas W. Götz, Kenneth M. Merz Jr., Darrin M. York, Hasan Metin Aktulga, Madushanka Manathunga
2025 J jnl
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.
J. Chem. Inf. Model.
Jinzhe Zeng, Timothy J. Giese, Duo Zhang, Han Wang, Darrin M. York
2025 J jnl
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.
J. Chem. Inf. Model.
Timothy J. Giese, Ryan Snyder, Zeke Piskulich, German P. Barletta, Shi Zhang, Erika McCarthy, Sölen Ekesan, Darrin M. York
2025 J jnl
Recent Developments in Amber Biomolecular Simulations.
J. Chem. Inf. Model.
David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed, George M. Giambasu, Timothy J. Giese, Andreas W. Götz, Julie A. Harris, Koushik Kasavajhala, Tai-Sung Lee, Zhen Li, Charles Lin, Jian Liu, Yinglong Miao, Romelia Salomón-Ferrer, Jana Shen, Ryan Snyder, Jason M. Swails, Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham III, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2024 J jnl
Dflow, a Python framework for constructing cloud-native AI-for-Science workflows.
CoRR
Xinzijian Liu, Yanbo Han, Zhuoyuan Li, Jiahao Fan, Chengqian Zhang, Jinzhe Zeng, Yifan Shan, Yannan Yuan, Wei-Hong Xu, Yun-Pei Liu, Yuzhi Zhang, Tongqi Wen, Darrin M. York, Zhicheng Zhong, Hang Zheng, Jun Cheng, Linfeng Zhang, Han Wang
2024 J jnl
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.
J. Chem. Inf. Model.
Hsu-Chun Tsai, James Xu, Zhenyu Guo, Yinhui Yi, Chuan Tian, Xinyu Que, Timothy J. Giese, Tai-Sung Lee, Darrin M. York, Abir Ganguly, Albert C. Pan
2023 J jnl
AmberTools.
J. Chem. Inf. Model.
David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2022 J jnl
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).
J. Chem. Inf. Model.
Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J. Giese, Darrin M. York
2021 J jnl
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
J. Chem. Inf. Model.
Han Zhang, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im
2020 J jnl
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
J. Chem. Inf. Model.
Tai-Sung Lee, Bryce K. Allen, Timothy J. Giese, Zhenyu Guo, Pengfei Li, Charles Lin, T. Dwight McGee Jr., David A. Pearlman, Brian K. Radak, Yujun Tao, Hsu-Chun Tsai, Huafeng Xu, Woody Sherman, Darrin M. York
2020 J jnl
Validation of Free Energy Methods in AMBER.
J. Chem. Inf. Model.
Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M. Merz Jr., Darrin M. York
2019 J jnl
Using AMBER18 for Relative Free Energy Calculations.
J. Chem. Inf. Model.
Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.
2018 J jnl
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
J. Chem. Inf. Model.
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
2016 B conf
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations.
ICPP
Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
2016 J jnl
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations.
CoRR
Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
2016 J jnl
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.
J. Comput. Aided Mol. Des.
Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo
2015 J jnl
Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg
J. Comput. Chem.
Maria T. Panteva, George M. Giambasu, Darrin M. York
2015 J jnl
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models.
J. Comput. Chem.
Ming Huang, Timothy J. Giese, Darrin M. York
2013 — conf
A framework for flexible and scalable replica-exchange on production distributed CI.
XSEDE
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
2009 J jnl
CHARMM: The biomolecular simulation program.
J. Comput. Chem.
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, Victor 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
2008 J jnl
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.
J. Comput. Chem.
Timothy J. Giese, Darrin M. York
2007 J jnl
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.
J. Comput. Chem.
Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York
2006 J jnl
A charge-scaling implementation of the variational electrostatic projection method.
J. Comput. Chem.
Brent A. Gregersen, Darrin M. York
2003 J jnl
Fast approximate methods for calculating nucleic acid base pair interaction energies.
J. Comput. Chem.
Edward C. Sherer, Darrin M. York, Christopher J. Cramer
2000 J jnl
Electronic structure properties of solvated biomolecules: A quantum approach for macromolecular characterization.
J. Comput. Chem.
Jana Khandogin, Anguang Hu, Darrin M. York
1994 J jnl
Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc.
J. Comput. Chem.
Darrin M. York, Lee J. Bartolotti, Thomas A. Darden, Lee G. Pedersen, M. W. Anderson