Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations. - Wei Pan; Tai-Sung Lee; Weitao Yang (J. Comput. Chem., 1998)

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. - Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C. Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo 001; Tai-Sung Lee; James W. Caldwell; Junmei Wang; et al. (J. Comput. Chem., 2003)

A framework for flexible and scalable replica-exchange on production distributed CI. - 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 (XSEDE, 2013)

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. - Antons Treikalis; André Merzky; Haoyuan Chen; Tai-Sung Lee; Darrin M. York; Shantenu Jha (ICPP, 2016)

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. - Yuan Hu 002; Brad Sherborne; Tai-Sung Lee; David A. Case; Darrin M. York; Zhuyan Guo (J. Comput. Aided Mol. Des., 2016)

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. - 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 (J. Chem. Inf. Model., 2018)

Using AMBER18 for Relative Free Energy Calculations. - Lin Frank Song; Tai-Sung Lee; Chun Zhu; Darrin M. York; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. - Tai-Sung Lee; Bryce K. Allen; Timothy J. Giese; Zhenyu Guo; Pengfei Li 003; Charles Lin; T. Dwight McGee Jr.; David A. Pearlman; Brian K. Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; et al. (J. Chem. Inf. Model., 2020)

Validation of Free Energy Methods in AMBER. - Hsu-Chun Tsai; Yujun Tao; Tai-Sung Lee; Kenneth M. Merz Jr.; Darrin M. York (J. Chem. Inf. Model., 2020)

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. - Han Zhang 028; Seonghoon Kim; Timothy J. Giese; Tai-Sung Lee; Jumin Lee; Darrin M. York; Wonpil Im (J. Chem. Inf. Model., 2021)

AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). - Abir Ganguly; Hsu-Chun Tsai; Mario Fernández-Pendás; Tai-Sung Lee; Timothy J. Giese; Darrin M. York (J. Chem. Inf. Model., 2022)

AmberTools. - 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; et al. (J. Chem. Inf. Model., 2023)

Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. - 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 (J. Chem. Inf. Model., 2024)

Recent Developments in Amber Biomolecular Simulations. - 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; et al. (J. Chem. Inf. Model., 2025)