Timothy J. Giese

13 papers Journal 13
YearRankTypeTitle / Venue / Authors
2026 J jnl
A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.
J. Chem. Inf. Model.
Hsu-Chun Tsai, Shi Zhang, Tai-Sung Lee, Timothy J. Giese, Charles Lin, James Xu, Yinhui Yi, Darrin M. York, Abir Ganguly, Albert C. Pan
2026 J jnl
Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization.
J. Chem. Inf. Model.
Alejandro Blanco-Gonzalez, William Betancourt, Ryan Snyder, Shi Zhang, Timothy J. Giese, Zeke Piskulich, Andreas W. Götz, Kenneth M. Merz Jr., Darrin M. York, Hasan Metin Aktulga, Madushanka Manathunga
2025 J jnl
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.
J. Chem. Inf. Model.
Jinzhe Zeng, Timothy J. Giese, Duo Zhang, Han Wang, Darrin M. York
2025 J jnl
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.
J. Chem. Inf. Model.
Timothy J. Giese, Ryan Snyder, Zeke Piskulich, German P. Barletta, Shi Zhang, Erika McCarthy, Sölen Ekesan, Darrin M. York
2025 J jnl
Recent Developments in Amber Biomolecular Simulations.
J. Chem. Inf. Model.
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.
2024 J jnl
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.
J. Chem. Inf. Model.
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
2023 J jnl
AmberTools.
J. Chem. Inf. Model.
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.
2022 J jnl
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).
J. Chem. Inf. Model.
Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J. Giese, Darrin M. York
2021 J jnl
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
J. Chem. Inf. Model.
Han Zhang, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im
2020 J jnl
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
J. Chem. Inf. Model.
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
2018 J jnl
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
J. Chem. Inf. Model.
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
2015 J jnl
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models.
J. Comput. Chem.
Ming Huang, Timothy J. Giese, Darrin M. York
2008 J jnl
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.
J. Comput. Chem.
Timothy J. Giese, Darrin M. York