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)

Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models. - Ming Huang 006; Timothy J. Giese; Darrin M. York (J. Comput. Chem., 2015)

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)

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)

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)

FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks. - Timothy J. Giese; Ryan Snyder; Zeke Piskulich; German P. Barletta; Shi Zhang; Erika McCarthy; Sölen Ekesan; Darrin M. York (J. Chem. Inf. Model., 2025)

DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials. - Jinzhe Zeng; Timothy J. Giese; Duo Zhang; Han Wang 006; Darrin M. York (J. Chem. Inf. Model., 2025)