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)

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)

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)

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

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; 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)

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)

Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models - Ming Huang; Timothy J. Giese; Darrin M. York (J. Comput. Chem., 2015)

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities - Timothy J. Giese; Darrin M. York (J. Comput. Chem., 2008)