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Timothy J. Giese, Ph.D. - Publications

Affiliations: 
2005 University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Physical Chemistry, Molecular Physics
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Giese TJ, Ekesan Ş, McCarthy E, Tao Y, York DM. Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of Chemical Theory and Computation. PMID 38367218 DOI: 10.1021/acs.jctc.3c01401  0.576
2023 Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153  0.5
2023 Giese TJ, York DM. 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. PMID 37125722 DOI: 10.1063/5.0147218  0.582
2023 McCarthy E, Ekesan Ş, Giese TJ, Wilson TJ, Deng J, Huang L, Lilley DMJ, York DM. Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology. Nucleic Acids Research. PMID 37070188 DOI: 10.1093/nar/gkad260  0.61
2023 Zeng J, Tao Y, Giese TJ, York DM. Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states. The Journal of Chemical Physics. 158: 124110. PMID 37003741 DOI: 10.1063/5.0139281  0.735
2023 Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society. PMID 36706353 DOI: 10.1021/jacs.2c10079  0.513
2023 Zeng J, Tao Y, Giese TJ, York DM. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of Chemical Theory and Computation. PMID 36696673 DOI: 10.1021/acs.jctc.2c01172  0.756
2023 Tsai HC, Lee TS, Ganguly A, Giese TJ, Ebert MC, Labute P, Merz KM, York DM. AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways. Journal of Chemical Theory and Computation. PMID 36622640 DOI: 10.1021/acs.jctc.2c00725  0.565
2022 Ganguly A, Tsai HC, Fernández-Pendás M, Lee TS, Giese TJ, York DM. AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). Journal of Chemical Information and Modeling. PMID 36450130 DOI: 10.1021/acs.jcim.2c00879  0.582
2022 Giese TJ, Zeng J, York DM. Multireference Generalization of the Weighted Thermodynamic Perturbation Method. The Journal of Physical Chemistry. A. PMID 36301936 DOI: 10.1021/acs.jpca.2c06201  0.766
2022 Giese TJ, Zeng J, Ekesan Ş, York DM. 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. PMID 35709391 DOI: 10.1021/acs.jctc.2c00151  0.773
2021 Zeng J, Giese TJ, Ekesan Ş, York DM. 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: 6993-7009. PMID 34644071 DOI: 10.1021/acs.jctc.1c00201  0.746
2021 Zhang H, Kim S, Giese TJ, Lee TS, Lee J, York DM, Im W. CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. Journal of Chemical Information and Modeling. PMID 34521199 DOI: 10.1021/acs.jcim.1c00747  0.605
2021 Giese TJ, Ekesan Ş, York DM. Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis. The Journal of Physical Chemistry. A. PMID 33784093 DOI: 10.1021/acs.jpca.1c00736  0.569
2021 Giese TJ, York DM. Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. Journal of Chemical Theory and Computation. PMID 33528251 DOI: 10.1021/acs.jctc.0c01219  0.558
2020 Lee TS, Allen BK, Giese TJ, Guo Z, Li P, Lin C, McGee TD, Pearlman DA, Radak BK, Tao Y, Tsai HC, Xu H, Sherman W, York DM. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. Journal of Chemical Information and Modeling. PMID 32936637 DOI: 10.1021/Acs.Jcim.0C00613  0.612
2020 Ganguly A, Weissman BP, Giese TJ, Li NS, Hoshika S, Rao S, Benner SA, Piccirilli JA, York DM. Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nature Chemistry. PMID 31959957 DOI: 10.1038/S41557-019-0391-X  0.656
2019 Giese TJ, York DM. 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. PMID 31507179 DOI: 10.1021/Acs.Jctc.9B00401  0.666
2019 Gaines CS, Giese TJ, York DM. Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology. Acs Catalysis. 9: 5803-5815. PMID 31328021 DOI: 10.1021/Acscatal.9B01155  0.648
2018 Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg AE, Case DA, Walker RC, York DM. GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. Journal of Chemical Information and Modeling. PMID 30199633 DOI: 10.1021/Acs.Jcim.8B00462  0.626
2018 Giese TJ, York DM. A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method. Journal of Chemical Theory and Computation. PMID 29357243 DOI: 10.1021/Acs.Jctc.7B01175  0.656
2017 Giese TJ, York DM. Quantum mechanical force fields for condensed phase molecular simulations. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 29: 383002. PMID 28817382 DOI: 10.1088/1361-648X/Aa7C5C  0.685
2017 Huang M, Dissanayake T, Kuechler E, Radak BK, Lee TS, Giese TJ, York DM. A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations. Journal of Chemical Theory and Computation. PMID 28768099 DOI: 10.1021/Acs.Jctc.7B00161  0.753
2017 Chen H, Giese TJ, Golden BL, York DM. Divalent metal ion activation of a guanine general base in the hammerhead ribozyme: insights from molecular simulations. Biochemistry. PMID 28530384 DOI: 10.1021/Acs.Biochem.6B01192  0.727
2016 Giese TJ, York DM. The Ambient-Potential Composite Ewald Method for Ab Initio QM/MM Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. PMID 27171914 DOI: 10.1021/Acs.Jctc.6B00198  0.661
2016 Kuechler ER, Giese TJ, York DM. VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions. The Journal of Chemical Physics. 144: 164115. PMID 27131539 DOI: 10.1063/1.4946779  0.68
2015 Kuechler ER, Giese TJ, York DM. Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations. The Journal of Chemical Physics. 143: 234111. PMID 26696050 DOI: 10.1063/1.4937166  0.669
2015 Huang M, Giese TJ, York DM. Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models. Journal of Computational Chemistry. 36: 1370-89. PMID 25943338 DOI: 10.1002/Jcc.23933  0.743
2015 Giese TJ, Panteva MT, Chen H, York DM. Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field. Journal of Chemical Theory and Computation. 11: 451-461. PMID 25691830 DOI: 10.1021/Ct500799G  0.769
2015 Giese TJ, Panteva MT, Chen H, York DM. Multipolar Ewald Methods, 1: Theory, Accuracy, and Performance. Journal of Chemical Theory and Computation. 11: 436-450. PMID 25691829 DOI: 10.1021/Ct5007983  0.757
2014 Chen H, Giese TJ, Huang M, Wong KY, Harris ME, York DM. Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions. Chemistry (Weinheim An Der Bergstrasse, Germany). 20: 14336-43. PMID 25223953 DOI: 10.1002/Chem.201403862  0.804
2014 Giese TJ, Huang M, Chen H, York DM. Recent advances toward a general purpose linear-scaling quantum force field. Accounts of Chemical Research. 47: 2812-20. PMID 24937206 DOI: 10.1021/Ar500103G  0.807
2014 Heldenbrand H, Janowski PA, Giamba?u G, Giese TJ, Wedekind JE, York DM. Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. Journal of the American Chemical Society. 136: 7789-92. PMID 24842535 DOI: 10.1021/Ja500180Q  0.583
2014 Huang M, Giese TJ, Lee TS, York DM. Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods. Journal of Chemical Theory and Computation. 10: 1538-1545. PMID 24803866 DOI: 10.1021/Ct401013S  0.732
2014 Giese TJ, Chen H, Huang M, York DM. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions. Journal of Chemical Theory and Computation. 10: 1086-1098. PMID 24803856 DOI: 10.1021/Ct401035T  0.797
2013 Giese TJ, Chen H, Dissanayake T, Giamba?u GM, Heldenbrand H, Huang M, Kuechler ER, Lee TS, Panteva MT, Radak BK, York DM. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields. Journal of Chemical Theory and Computation. 9: 1417-1427. PMID 23814506 DOI: 10.1021/Ct3010134  0.8
2012 Giese TJ, York DM. Density-functional expansion methods: Grand challenges. Theoretical Chemistry Accounts. 131. PMID 27293378 DOI: 10.1007/S00214-012-1145-7  0.617
2012 Kaminski S, Giese TJ, Gaus M, York DM, Elstner M. Extended polarization in third-order SCC-DFTB from chemical-potential equalization. The Journal of Physical Chemistry. A. 116: 9131-41. PMID 22894819 DOI: 10.1021/Jp306239C  0.627
2012 Giese TJ, York DM. Density-functional expansion methods: Grand challenges Theoretical Chemistry Accounts. 131: 1-17. DOI: 10.1007/s00214-012-1145-7  0.516
2011 Giese TJ, York DM. Density-functional expansion methods: generalization of the auxiliary basis. The Journal of Chemical Physics. 134: 194103. PMID 21599040 DOI: 10.1063/1.3587052  0.603
2010 Giese TJ, York DM. Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations. The Journal of Chemical Physics. 133: 244107. PMID 21197976 DOI: 10.1063/1.3515479  0.622
2008 Giese TJ, York DM. Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tables. The Journal of Chemical Physics. 129: 016102. PMID 18624505 DOI: 10.1063/1.2945897  0.629
2008 Giese TJ, York DM. Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. Journal of Computational Chemistry. 29: 1895-904. PMID 18432622 DOI: 10.1002/Jcc.20946  0.633
2008 Giese TJ, York DM. Contracted auxiliary Gaussian basis integral and derivative evaluation. The Journal of Chemical Physics. 128: 064104. PMID 18282025 DOI: 10.1063/1.2821745  0.565
2007 Giese TJ, York DM. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations. The Journal of Chemical Physics. 127: 194101. PMID 18035873 DOI: 10.1063/1.2778428  0.651
2006 Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, de Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM. QCRNA 1.0: a database of quantum calculations for RNA catalysis. Journal of Molecular Graphics & Modelling. 25: 423-33. PMID 16580853 DOI: 10.1016/J.Jmgm.2006.02.011  0.729
2005 Giese TJ, Sherer EC, Cramer CJ, York DM. A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs. Journal of Chemical Theory and Computation. 1: 1275-85. PMID 26631671 DOI: 10.1021/Ct050102L  0.617
2005 Giese TJ, York DM. Improvement of semiempirical response properties with charge-dependent response density. The Journal of Chemical Physics. 123: 164108. PMID 16268682 DOI: 10.1063/1.2080007  0.67
2005 Giese TJ, Sherer EC, Cramer CJ, York DM. A semiempirical quantum model for hydrogen-bonded nucleic acid base pairs Journal of Chemical Theory and Computation. 1: 1275-1285. DOI: 10.1021/ct050102l  0.533
2004 Giese TJ, York DM. Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits. The Journal of Chemical Physics. 120: 9903-6. PMID 15268007 DOI: 10.1063/1.1756583  0.6
2004 Giese TJ, York DM. Design and application of a multicoefficient correlation method for dispersion interactions. The Journal of Chemical Physics. 120: 590-602. PMID 15267893 DOI: 10.1063/1.1630955  0.634
2004 Giese TJ, York DM. Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields. The Journal of Chemical Physics. 120: 7939-48. PMID 15267709 DOI: 10.1063/1.1690232  0.618
2004 Giese TJ, York DM. High-level ab initio methods for calculation of potential energy surfaces of van der Waals complexes International Journal of Quantum Chemistry. 98: 388-408. DOI: 10.1002/Qua.20074  0.67
2003 Giese TJ, Audette VM, York DM. Examination of the correlation energy and second virial coefficients from accurate ab initio calculations of rare-gas dimers Journal of Chemical Physics. 119: 2618-2622. DOI: 10.1063/1.1587684  0.664
2001 Cramer CJ, Kormos BL, Winget P, Audette VM, Beebe JM, Brauer CS, Burdick WR, Cochran EW, Eklov BL, Giese TJ, Jun Y, Kesavan LSD, Kinsinger CR, Minyaev ME, Rajamani R, et al. A Cooperative Molecular Modeling Exercise—The Hypersurface as Classroom Journal of Chemical Education. 78: 1202. DOI: 10.1021/Ed078P1202  0.39
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