Timothy J. Giese

Rutgers Sexual and Reproductive Health and Rights — Netherlands

Biochemistry, Genetics and Molecular Biology · Life Sciences

31h-index4.4kcitations78works12.52yr avg
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Research Topics

Protein Structure and Dynamics(35), Spectroscopy and Quantum Chemical Studies(23), Machine Learning in Materials Science(21), Advanced Chemical Physics Studies(19), RNA and protein synthesis mechanisms(19)

Publications78 total

A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules
Journal of Chemical Information and Modeling·2026
Recent Developments in Amber Biomolecular Simulations
Journal of Chemical Information and Modeling·2025· 35 citedOpen Access
Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications
The Journal of Physical Chemistry B·2025· 6 citedOpen Access
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks
Journal of Chemical Information and Modeling·2025· 3 citedOpen Access
DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials
Journal of Chemical Theory and Computation·2025· 46 citedOpen Access
The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions
Scientific Data·2025· 4 citedOpen Access
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials
Journal of Chemical Information and Modeling·2025· 15 citedOpen Access
The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme
ACS Catalysis·2024· 7 citedOpen Access
Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization
2024
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
Journal of Chemical Information and Modeling·2024· 6 citedOpen Access
Software Infrastructure for Next-Generation QM/MM−ΔMLP Force Fields
The Journal of Physical Chemistry B·2024· 22 citedOpen Access
Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials
The Journal of Chemical Physics·2024· 14 cited
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·2024· 5 citedOpen Access
Alchemical Enhanced Sampling with Optimized Phase Space Overlap
Journal of Chemical Theory and Computation·2024· 14 citedOpen Access
Surface-Accelerated String Method for Locating Minimum Free Energy Paths
Journal of Chemical Theory and Computation·2024· 11 citedOpen Access
AmberTools
Journal of Chemical Information and Modeling·2023· 1.6k citedOpen Access
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations
The Journal of Chemical Physics·2023· 4 citedOpen Access
Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology
Nucleic Acids Research·2023· 13 citedOpen Access
Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states
The Journal of Chemical Physics·2023· 24 citedOpen Access
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis
Journal of the American Chemical Society·2023· 9 citedOpen Access
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Frequent Co-authors

Darrin M. York(50), Tai‐Sung Lee(13), Jinzhe Zeng(9), Ming Huang(7), Haoyuan Chen(7), Yujun Tao(4), Hsu‐Chun Tsai(4), Şölen Ekesan(4), Abir Ganguly(4), David A. Case(3), David S. Cerutti(3), Adrián E. Roitberg(3), Kenneth M. Merz(3), Brian K. Radak(3), George M. Giambaşu(3), Erich R. Kuechler(3), Maria T. Panteva(3), Vinícius Wilian D. Cruzeiro(2), Koushik Kasavajhala(2), Jian Liu(2)