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2020 – today
- 2024
[j11]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:
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. J. Chem. Inf. Model. 64(18): 7046-7055 (2024)- 2023
- [j10]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.:
AmberTools. J. Chem. Inf. Model. 63(20): 6183-6191 (2023) - 2022
- [j9]Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J. Giese, Darrin M. York:
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). J. Chem. Inf. Model. 62(23): 6069-6083 (2022) - 2021
- [j8]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
- [j7]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) - [j6]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:
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
- [j5]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
- [j4]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
- [j3]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) - 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
- 2003
- [j2]Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Tai-Sung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman:
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24(16): 1999-2012 (2003)
1990 – 1999
- 1998
- [j1]Wei Pan, Tai-Sung Lee, Weitao Yang:
Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations. J. Comput. Chem. 19(9): 1101-1109 (1998)
Coauthor Index
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