Timothy J. Giese

According to our database, Timothy J. Giese authored at least 11 papers between 2008 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.

Jinzhe Zeng, Timothy J. Giese, Duo Zhang, Han Wang, Darrin M. York

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

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, 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.

J. Chem. Inf. Model., 2025

2024

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

2023

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, 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.

J. Chem. Inf. Model., October, 2023

2022

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

2021

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

2020

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, Woody Sherman, Darrin M. York

J. Chem. Inf. Model., 2020

2018

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

2015

Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models.

Ming Huang, Timothy J. Giese, Darrin M. York

J. Comput. Chem., 2015

2008

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