Timothy J Giese (Timothy Giese)

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 35

Top Topics

Particulate Matter

Machine Learning

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

Journal of the American Chemical Society

The Journal of chemical physics

Journal of chemical information and modeling

This page only lists publications with an associated author ORCID identifier.

Publications

Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B 128 (26) (2024)
Yujun Tao, Timothy J Giese, Darrin M York
Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules (Basel, Switzerland) 29 (11) (2024)
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation 20 (9) (2024)
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 Pan
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. Journal of chemical information and modeling (2024)
Yujun Tao, Timothy J Giese, Darrin M York
Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules (Basel, Switzerland) 29 (11) (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Yujun Tao, Timothy J Giese, Darrin M York
Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules (Basel, Switzerland) 29 (11) (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation 20 (9) (2024)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states. The Journal of chemical physics 158 (12) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, Gerardo Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C 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 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 L Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz
AmberTools. Journal of chemical information and modeling (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J Giese, Maximilian Ccjc Ebert, Paul Labute, Kenneth M Merz, Darrin M York
AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways. Journal of chemical theory and computation (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Timothy J Giese, Jinzhe Zeng, Şölen Ekesan, Darrin M York
Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions. Journal of chemical theory and computation 18 (7) (2022)
Timothy J Giese, Jinzhe Zeng, Darrin M York
Multireference Generalization of the Weighted Thermodynamic Perturbation Method. The journal of physical chemistry. A 126 (45) (2022)
Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J Giese, Darrin M York
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). Journal of chemical information and modeling (2022)
Han Zhang, Seonghoon Kim, Timothy J Giese, Tai-Sung Lee, Jumin Lee, Darrin M York, Wonpil Im
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. Journal of chemical information and modeling 61 (9) (2021)
Jinzhe Zeng, Timothy J Giese, Şölen Ekesan, Darrin M York
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution. Journal of chemical theory and computation 17 (11) (2021)