Timothy J. Giese, Ph.D.

Affiliations: 
2005 University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Physical Chemistry, Molecular Physics
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Darrin M. York grad student 2005 UMN
 (Development and validation of new-generation molecular mechanical force fields and semiempirical Hamiltonians.)
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Publications

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Giese TJ, York DM. (2021) Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. Journal of Chemical Theory and Computation
Lee TS, Allen BK, Giese TJ, et al. (2020) Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. Journal of Chemical Information and Modeling
Ganguly A, Weissman BP, Giese TJ, et al. (2020) Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nature Chemistry
Giese TJ, York DM. (2019) Development of a Robust Indirect Approach for MM→QM Free Energy Calculations that Combines Force-matched Reference Potential and Bennett's Acceptance Ratio Methods. Journal of Chemical Theory and Computation
Gaines CS, Giese TJ, York DM. (2019) Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology. Acs Catalysis. 9: 5803-5815
Lee TS, Cerutti DS, Mermelstein D, et al. (2018) GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. Journal of Chemical Information and Modeling
Giese TJ, York DM. (2018) A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method. Journal of Chemical Theory and Computation
Giese TJ, York DM. (2017) Quantum mechanical force fields for condensed phase molecular simulations. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 29: 383002
Huang M, Dissanayake T, Kuechler E, et al. (2017) A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations. Journal of Chemical Theory and Computation
Chen H, Giese TJ, Golden BL, et al. (2017) Divalent metal ion activation of a guanine general base in the hammerhead ribozyme: insights from molecular simulations. Biochemistry
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