| Year |
Citation |
Score |
| 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, ... ... York DM, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153 |
0.734 |
|
| 2023 |
Zeng J, Zhang D, Lu D, Mo P, Li Z, Chen Y, Rynik M, Huang L, Li Z, Shi S, Wang Y, Ye H, Tuo P, Yang J, Ding Y, ... ... York DM, et al. DeePMD-kit v2: A software package for deep potential models. The Journal of Chemical Physics. 159. PMID 37526163 DOI: 10.1063/5.0155600 |
0.74 |
|
| 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 |
0.713 |
|
| 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 |
0.732 |
|
| 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 |
0.808 |
|
| 2023 |
Xu Y, Harris ME, York DM, Wong KY. Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. Journal of Chemical Theory and Computation. PMID 36753428 DOI: 10.1021/acs.jctc.2c01277 |
0.577 |
|
| 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 |
0.664 |
|
| 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 |
0.817 |
|
| 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 |
0.673 |
|
| 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 |
0.679 |
|
| 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 |
0.823 |
|
| 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 |
0.829 |
|
| 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 |
0.814 |
|
| 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 |
0.693 |
|
| 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 |
0.675 |
|
| 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 |
0.665 |
|
| 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 |
0.702 |
|
| 2020 |
Lee TS, Lin Z, Allen BK, Lin C, Radak BK, Tao Y, Tsai HC, Sherman W, York DM. Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials. Journal of Chemical Theory and Computation. PMID 32672455 DOI: 10.1021/Acs.Jctc.0C00237 |
0.368 |
|
| 2020 |
Tsai HC, Tao Y, Lee TS, Merz KM, York DM. Validation of Free Energy Methods in AMBER. Journal of Chemical Information and Modeling. PMID 32551593 DOI: 10.1021/Acs.Jcim.0C00285 |
0.37 |
|
| 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 |
0.737 |
|
| 2019 |
Ganguly A, Weissman BP, Piccirilli JA, York DM. Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme. Acs Catalysis. 9: 10612-10617. PMID 31840007 DOI: 10.1021/Acscatal.9B02035 |
0.338 |
|
| 2019 |
Ekesan Ş, York DM. Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Research. PMID 31511899 DOI: 10.1093/Nar/Gkz773 |
0.421 |
|
| 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 |
0.733 |
|
| 2019 |
Kostenbader K, York DM. Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. Rna (New York, N.Y.). PMID 31363004 DOI: 10.1261/Rna.071944.119 |
0.452 |
|
| 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 |
0.742 |
|
| 2019 |
Song LF, Lee TS, Zhu C, York DM, Merz KM. Using AMBER18 for Relative Free Energy Calculations. Journal of Chemical Information and Modeling. PMID 31244091 DOI: 10.1021/Acs.Jcim.9B00105 |
0.379 |
|
| 2019 |
Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM. An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. Acs Chemical Biology. PMID 31095369 DOI: 10.1021/Acschembio.9B00202 |
0.356 |
|
| 2019 |
Ekesan Ş, York DM. A Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation. The Journal of Physical Chemistry. B. PMID 31002511 DOI: 10.1021/Acs.Jpcb.8B11923 |
0.313 |
|
| 2019 |
Li X, York DM, Meyer MP. Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction. The Journal of Physical Chemistry. A. PMID 30855141 DOI: 10.1021/Acs.Jpca.9B00172 |
0.686 |
|
| 2019 |
Giambasu GM, Case DA, York DM. Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory. Journal of the American Chemical Society. PMID 30632365 DOI: 10.1021/Jacs.8B11474 |
0.791 |
|
| 2018 |
König G, Brooks BR, Thiel W, York DM. On the convergence of multi-scale free energy simulations. Molecular Simulation. 44: 1062-1081. PMID 30581251 DOI: 10.1080/08927022.2018.1475741 |
0.565 |
|
| 2018 |
König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules (Basel, Switzerland). 23. PMID 30347691 DOI: 10.3390/Molecules23102695 |
0.626 |
|
| 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 |
0.715 |
|
| 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 |
0.727 |
|
| 2017 |
Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation. Methods in Enzymology. 596: 433-457. PMID 28911780 DOI: 10.1016/Bs.Mie.2017.07.017 |
0.348 |
|
| 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 |
0.736 |
|
| 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 |
0.784 |
|
| 2017 |
Gaines CS, York DM. Model for the Functional Active State of the TS Ribozyme from Molecular Simulation. Angewandte Chemie (International Ed. in English). PMID 28763583 DOI: 10.1002/Anie.201705608 |
0.417 |
|
| 2017 |
Lee T, Hu Y, Sherborne BS, Guo Z, York DM. Towards fast and accurate binding affinity prediction with pmemdGTI: an efficient implementation of GPU-accelerated Thermodynamic Integration. Journal of Chemical Theory and Computation. PMID 28618232 DOI: 10.1021/Acs.Jctc.7B00102 |
0.321 |
|
| 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 |
0.802 |
|
| 2016 |
Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. Acs Catalysis. 6: 1853-1869. PMID 27774349 DOI: 10.1021/Acscatal.5B02158 |
0.438 |
|
| 2016 |
Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallographica. Section D, Structural Biology. 72: 1062-72. PMID 27599738 DOI: 10.1107/S2059798316012225 |
0.343 |
|
| 2016 |
Hu Y, Sherborne B, Lee TS, Case DA, York DM, Guo Z. The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. Journal of Computer-Aided Molecular Design. PMID 27480697 DOI: 10.1007/S10822-016-9920-5 |
0.336 |
|
| 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 |
0.737 |
|
| 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 |
0.738 |
|
| 2016 |
Gaines CS, York DM. Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation. Journal of the American Chemical Society. PMID 26859432 DOI: 10.1021/Jacs.5B12061 |
0.415 |
|
| 2016 |
Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2.) Chemical Communications (Cambridge, England). PMID 26859380 DOI: 10.1039/C5Cc10212J |
0.664 |
|
| 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 |
0.737 |
|
| 2015 |
Panteva MT, Giambaşu GM, York DM. Force Field for Mg(2+), Mn(2+), Zn(2+) and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids. The Journal of Physical Chemistry. B. PMID 26583536 DOI: 10.1021/Acs.Jpcb.5B10423 |
0.804 |
|
| 2015 |
Radak BK, Romanus M, Lee TS, Chen H, Huang M, Treikalis A, Balasubramanian V, Jha S, York DM. Characterization of the Three-Dimensional Free Energy Manifold for the Uracil Ribonucleoside from Asynchronous Replica Exchange Simulations. Journal of Chemical Theory and Computation. 11: 373-377. PMID 26580900 DOI: 10.1021/Ct500776J |
0.735 |
|
| 2015 |
Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. Rna (New York, N.Y.). PMID 26567314 DOI: 10.1261/Rna.053710.115 |
0.797 |
|
| 2015 |
Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. Journal of the American Chemical Society. PMID 26517731 DOI: 10.1021/Jacs.5B08395 |
0.791 |
|
| 2015 |
Giambaşu GM, Gebala MK, Panteva MT, Luchko T, Case DA, York DM. Competitive interaction of monovalent cations with DNA from 3D-RISM. Nucleic Acids Research. 43: 8405-15. PMID 26304542 DOI: 10.1093/Nar/Gkv830 |
0.795 |
|
| 2015 |
Radak BK, Lee TS, Harris ME, York DM. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. Rna (New York, N.Y.). 21: 1566-77. PMID 26170378 DOI: 10.1261/Rna.051466.115 |
0.446 |
|
| 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 |
0.778 |
|
| 2015 |
Kellerman DL, Simmons KS, Pedraza M, Piccirilli JA, York DM, Harris ME. Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Analytical Biochemistry. 483: 12-20. PMID 25937290 DOI: 10.1016/J.Ab.2015.04.024 |
0.362 |
|
| 2015 |
Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochimica Et Biophysica Acta. PMID 25936517 DOI: 10.1016/J.Bbapap.2015.04.022 |
0.409 |
|
| 2015 |
Weissman BP, Li NS, York D, Harris M, Piccirilli JA. Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochimica Et Biophysica Acta. PMID 25828952 DOI: 10.1016/J.Bbapap.2015.03.007 |
0.332 |
|
| 2015 |
Chen H, Piccirilli JA, Harris ME, York DM. Effect of Zn(2+) binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects. Biochimica Et Biophysica Acta. PMID 25812974 DOI: 10.1016/J.Bbapap.2015.02.022 |
0.698 |
|
| 2015 |
Giamba?u GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. Rna (New York, N.Y.). 21: 963-74. PMID 25805858 DOI: 10.1261/Rna.047357.114 |
0.397 |
|
| 2015 |
Panteva MT, Giamba?u GM, York DM. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations. Journal of Computational Chemistry. 36: 970-82. PMID 25736394 DOI: 10.1002/Jcc.23881 |
0.415 |
|
| 2015 |
Panteva MT, Dissanayake T, Chen H, Radak BK, Kuechler ER, Giamba?u GM, Lee TS, York DM. Multiscale methods for computational RNA enzymology. Methods in Enzymology. 553: 335-74. PMID 25726472 DOI: 10.1016/Bs.Mie.2014.10.064 |
0.721 |
|
| 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 |
0.808 |
|
| 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 |
0.79 |
|
| 2015 |
Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry. 54: 1307-13. PMID 25615525 DOI: 10.1021/Bi5012833 |
0.352 |
|
| 2015 |
Radak BK, Romanus M, Lee TS, Chen H, Huang M, Treikalis A, Balasubramanian V, Jha S, York DM. Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations Journal of Chemical Theory and Computation. 11: 373-377. DOI: 10.1021/ct500776j |
0.444 |
|
| 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 |
0.824 |
|
| 2014 |
Kellerman DL, York DM, Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Current Opinion in Chemical Biology. 21: 96-102. PMID 25023967 DOI: 10.1016/J.Cbpa.2014.06.010 |
0.427 |
|
| 2014 |
Huang M, York DM. Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations. Physical Chemistry Chemical Physics : Pccp. 16: 15846-55. PMID 24961771 DOI: 10.1039/C4Cp01050G |
0.571 |
|
| 2014 |
Pabis A, Geronimo I, York DM, Paneth P. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field. Journal of Chemical Theory and Computation. 10: 2246-2254. PMID 24955078 DOI: 10.1021/Ct500205Z |
0.338 |
|
| 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 |
0.826 |
|
| 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 |
0.714 |
|
| 2014 |
Wong KY, Xu Y, York DM. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. Journal of Computational Chemistry. 35: 1302-16. PMID 24841935 DOI: 10.1002/Jcc.23628 |
0.658 |
|
| 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 |
0.771 |
|
| 2014 |
Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. Journal of Chemical Theory and Computation. 10: 1341-1352. PMID 24803862 DOI: 10.1021/Ct401042B |
0.374 |
|
| 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 |
0.819 |
|
| 2014 |
Giamba?u GM, Luchko T, Herschlag D, York DM, Case DA. Ion counting from explicit-solvent simulations and 3D-RISM. Biophysical Journal. 106: 883-94. PMID 24559991 DOI: 10.1016/J.Bpj.2014.01.021 |
0.41 |
|
| 2014 |
Kuechler ER, York DM. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl. The Journal of Chemical Physics. 140: 054109. PMID 24511924 DOI: 10.1063/1.4863344 |
0.426 |
|
| 2014 |
Lee TS, Radak BK, Huang M, Wong KY, York DM. Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach. Journal of Chemical Theory and Computation. 10: 24-34. PMID 24505217 DOI: 10.1021/Ct400691F |
0.688 |
|
| 2014 |
Kuechler ER, York DM. Publisher's Note: “Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl− attack on CH3Cl” [J. Chem. Phys. 140, 054109 (2014)] The Journal of Chemical Physics. 140: 099901. DOI: 10.1063/1.4867485 |
0.301 |
|
| 2013 |
Lee TS, Wong KY, Giambasu GM, York DM. Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. Progress in Molecular Biology and Translational Science. 120: 25-91. PMID 24156941 DOI: 10.1016/B978-0-12-381286-5.00002-0 |
0.796 |
|
| 2013 |
Gu H, Zhang S, Wong KY, Radak BK, Dissanayake T, Kellerman DL, Dai Q, Miyagi M, Anderson VE, York DM, Piccirilli JA, Harris ME. Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 110: 13002-7. PMID 23878223 DOI: 10.1073/Pnas.1215086110 |
0.632 |
|
| 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 |
0.821 |
|
| 2013 |
Lee TS, Radak BK, Pabis A, York DM. A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations. Journal of Chemical Theory and Computation. 9: 153-164. PMID 23457427 DOI: 10.1021/Ct300703Z |
0.382 |
|
| 2013 |
Radak BK, Harris ME, York DM. Molecular simulations of RNA 2'-O-transesterification reaction models in solution. The Journal of Physical Chemistry. B. 117: 94-103. PMID 23214417 DOI: 10.1021/Jp3084277 |
0.483 |
|
| 2013 |
Radak BK, Romanus M, Gallicchio E, Lee TS, Weidner O, Deng NJ, He P, Dai W, York DM, Levy RM, Jha S. A framework for flexible and scalable replica-exchange on production distributed CI Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484830 |
0.357 |
|
| 2012 |
Giese TJ, York DM. Density-functional expansion methods: Grand challenges. Theoretical Chemistry Accounts. 131. PMID 27293378 DOI: 10.1007/S00214-012-1145-7 |
0.691 |
|
| 2012 |
Wong KY, York DM. Exact Relation between Potential of Mean Force and Free-Energy Profile. Journal of Chemical Theory and Computation. 8: 3998-4003. PMID 23185141 DOI: 10.1021/Ct300392F |
0.609 |
|
| 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 |
0.702 |
|
| 2012 |
GiambaÅŸu GM, Lee TS, Scott WG, York DM. Mapping L1 ligase ribozyme conformational switch. Journal of Molecular Biology. 423: 106-22. PMID 22771572 DOI: 10.1016/J.Jmb.2012.06.035 |
0.362 |
|
| 2012 |
Wong KY, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment. Angewandte Chemie (International Ed. in English). 51: 647-51. PMID 22076983 DOI: 10.1002/Anie.201104147 |
0.673 |
|
| 2012 |
Giese TJ, York DM. Density-functional expansion methods: Grand challenges Theoretical Chemistry Accounts. 131: 1-17. DOI: 10.1007/s00214-012-1145-7 |
0.633 |
|
| 2011 |
Lee TS, Giamba?u G, Harris ME, York DM. Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path. The Journal of Physical Chemistry Letters. 2: 2538-2543. PMID 22200005 DOI: 10.1021/Jz201106Y |
0.373 |
|
| 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 |
0.685 |
|
| 2011 |
Wong KY, Lee TS, York DM. Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme. Journal of Chemical Theory and Computation. 7: 1-3. PMID 21379373 DOI: 10.1021/Ct100467T |
0.665 |
|
| 2011 |
Guza R, Kotandeniya D, Murphy K, Dissanayake T, Lin C, Giambasu GM, Lad RR, Wojciechowski F, Amin S, Sturla SJ, Hudson RH, York DM, Jankowiak R, Jones R, Tretyakova NY. Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA. Nucleic Acids Research. 39: 3988-4006. PMID 21245046 DOI: 10.1093/Nar/Gkq1341 |
0.761 |
|
| 2011 |
Wong K, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Inside Back Cover: Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment (Angew. Chem. Int. Ed. 3/2012) Angewandte Chemie International Edition. 51: 823-823. DOI: 10.1002/Anie.201108319 |
0.598 |
|
| 2011 |
Wong K, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Innenrücktitelbild: Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment (Angew. Chem. 3/2012) Angewandte Chemie. 124: 847-847. DOI: 10.1002/Ange.201108319 |
0.598 |
|
| 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 |
0.7 |
|
| 2010 |
Moser A, Range K, York DM. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. The Journal of Physical Chemistry. B. 114: 13911-21. PMID 20942500 DOI: 10.1021/Jp107450N |
0.736 |
|
| 2010 |
Lee TS, York DM. Computational mutagenesis studies of hammerhead ribozyme catalysis. Journal of the American Chemical Society. 132: 13505-18. PMID 20812715 DOI: 10.1021/Ja105956U |
0.326 |
|
| 2010 |
Formoso E, Matxain JM, Lopez X, York DM. Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes. The Journal of Physical Chemistry. B. 114: 7371-82. PMID 20455590 DOI: 10.1021/Jp909004Y |
0.431 |
|
| 2010 |
Giambasu GM, Lee TS, Sosa CP, Robertson MP, Scott WG, York DM. Identification of dynamical hinge points of the L1 ligase molecular switch. Rna (New York, N.Y.). 16: 769-80. PMID 20167653 DOI: 10.1261/Rna.1897810 |
0.795 |
|
| 2010 |
Seneviratne U, Antsypovich S, Goggin M, Dorr DQ, Guza R, Moser A, Thompson C, York DM, Tretyakova N. Exocyclic deoxyadenosine adducts of 1,2,3,4-diepoxybutane: synthesis, structural elucidation, and mechanistic studies. Chemical Research in Toxicology. 23: 118-33. PMID 19883087 DOI: 10.1021/Tx900312E |
0.558 |
|
| 2010 |
Lee TS, Giamba?u GM, York DM. Insights into the role of conformational transitions and metal ion binding in RNA catalysis from molecular simulations Annual Reports in Computational Chemistry. 6: 171-200. DOI: 10.1016/S1574-1400(10)06010-X |
0.41 |
|
| 2009 |
Moser A, Guza R, Tretyakova N, York DM. Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine. Theoretical Chemistry Accounts. 122: 179-188. PMID 19890472 DOI: 10.1007/S00214-008-0497-5 |
0.607 |
|
| 2009 |
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, ... ... York DM, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287 |
0.789 |
|
| 2009 |
Lee TS, Giamba?u GM, Sosa CP, Martick M, Scott WG, York DM. Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation. Journal of Molecular Biology. 388: 195-206. PMID 19265710 DOI: 10.1016/J.Jmb.2009.02.054 |
0.387 |
|
| 2009 |
York D. Hybrid Methods of Molecular Modeling Hybrid Methods of Molecular Modeling . By Andrei L. Tchougréeff (Lomonosov Moscow State University). From the series, Progress in Theoretical Chemistry and Physics. Edited by W. N. Lipscomb and Y. Chauvin (Honorary Editors) and J. Maruani and S. Wilson (Editors-in-Chief). Springer Science + Business Media B.V.: New York. 2008 . xvii + 344 pp. $449.00. ISBN 978-1-4020-8188-0 . Journal of the American Chemical Society. 131: 15565-15566. DOI: 10.1021/Ja906876N |
0.302 |
|
| 2008 |
Yang Y, Yu H, York D, Elstner M, Cui Q. Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. Journal of Chemical Theory and Computation. 4: 2067-2084. PMID 19352441 DOI: 10.1021/Ct800330D |
0.589 |
|
| 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 |
0.712 |
|
| 2008 |
Nam K, Gao J, York DM. Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases. Rna (New York, N.Y.). 14: 1501-7. PMID 18566190 DOI: 10.1261/Rna.863108 |
0.616 |
|
| 2008 |
Lee TS, York DM. Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations. Journal of the American Chemical Society. 130: 7168-9. PMID 18479101 DOI: 10.1021/Ja711242B |
0.318 |
|
| 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 |
0.707 |
|
| 2008 |
Martick M, Lee TS, York DM, Scott WG. Solvent structure and hammerhead ribozyme catalysis. Chemistry & Biology. 15: 332-42. PMID 18420140 DOI: 10.1016/J.Chembiol.2008.03.010 |
0.426 |
|
| 2008 |
Nam K, Gao J, York DM. Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. Journal of the American Chemical Society. 130: 4680-91. PMID 18345664 DOI: 10.1021/Ja0759141 |
0.632 |
|
| 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 |
0.666 |
|
| 2008 |
Lee TS, Silva López C, Giambasu GM, Martick M, Scott WG, York DM. Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation. Journal of the American Chemical Society. 130: 3053-64. PMID 18271579 DOI: 10.1021/Ja076529E |
0.815 |
|
| 2007 |
Nam K, Cui Q, Gao J, York DM. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms. Journal of Chemical Theory and Computation. 3: 486-504. PMID 26637030 DOI: 10.1021/Ct6002466 |
0.697 |
|
| 2007 |
Lee TS, López CS, Martick M, Scott WG, York DM. Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation. Journal of Chemical Theory and Computation. 3: 325-327. PMID 19079784 DOI: 10.1021/Ct6003142 |
0.38 |
|
| 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 |
0.72 |
|
| 2007 |
Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. The Journal of Physical Chemistry. A. 111: 10861-73. PMID 17914769 DOI: 10.1021/Jp074167R |
0.52 |
|
| 2007 |
Mayaan E, Moser A, MacKerell AD, York DM. CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. Journal of Computational Chemistry. 28: 495-507. PMID 17186477 DOI: 10.1002/Jcc.20474 |
0.811 |
|
| 2007 |
Nam K, Cui Q, Gao J, York DM. Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms Journal of Chemical Theory and Computation. 3: 486-504. DOI: 10.1021/ct6002466 |
0.453 |
|
| 2007 |
Nam K, Gao J, York DM. New QM/MM Models for Multiscale Simulation of Phosphoryl Transfer Reactions in Solution Multiscale Simulation Methods For Nanomaterials. 201-218. DOI: 10.1002/9780470191675.ch12 |
0.484 |
|
| 2006 |
Tejero I, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM, York DM. Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. The Journal of Physical Chemistry. B. 110: 24708-19. PMID 17134234 DOI: 10.1021/Jp066263I |
0.391 |
|
| 2006 |
Liu Y, Gregersen BA, Hengge A, York DM. Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory. Biochemistry. 45: 10043-53. PMID 16906762 DOI: 10.1021/Bi060869F |
0.803 |
|
| 2006 |
Lopez X, Dejaegere A, Leclerc F, York DM, Karplus M. Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. The Journal of Physical Chemistry. B. 110: 11525-39. PMID 16771429 DOI: 10.1021/Jp0603942 |
0.624 |
|
| 2006 |
Range K, Ayala I, York D, Barry BA. Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment. The Journal of Physical Chemistry. B. 110: 10970-81. PMID 16771350 DOI: 10.1021/Jp061503F |
0.603 |
|
| 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 |
0.799 |
|
| 2006 |
Range K, López CS, Moser A, York DM. Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer. The Journal of Physical Chemistry. A. 110: 791-7. PMID 16405355 DOI: 10.1021/Jp054360Q |
0.73 |
|
| 2006 |
Gregersen BA, York DM. A charge-scaling implementation of the variational electrostatic projection method. Journal of Computational Chemistry. 27: 103-15. PMID 16273506 DOI: 10.1002/Jcc.20318 |
0.806 |
|
| 2005 |
Nam K, Gao J, York DM. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations. Journal of Chemical Theory and Computation. 1: 2-13. PMID 26641110 DOI: 10.1021/Ct049941I |
0.621 |
|
| 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 |
0.702 |
|
| 2005 |
Liu Y, Gregersen BA, Lopez X, York DM. Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification. The Journal of Physical Chemistry. B. 109: 19987-20003. PMID 16853584 DOI: 10.1021/Jp053146Z |
0.819 |
|
| 2005 |
Xu D, Guo H, Liu Y, York DM. Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions. The Journal of Physical Chemistry. B. 109: 13827-34. PMID 16852731 DOI: 10.1021/Jp051042I |
0.427 |
|
| 2005 |
Gregersen BA, Khandogin J, Thiel W, York DM. Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution. The Journal of Physical Chemistry. B. 109: 9810-7. PMID 16852181 DOI: 10.1021/Jp044061L |
0.819 |
|
| 2005 |
Khandogin J, Gregersen BA, Thiel W, York DM. Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation. The Journal of Physical Chemistry. B. 109: 9799-809. PMID 16852180 DOI: 10.1021/Jp044062D |
0.827 |
|
| 2005 |
Gregersen BA, York DM. Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations. The Journal of Physical Chemistry. B. 109: 536-56. PMID 16851046 DOI: 10.1021/Jp0469968 |
0.813 |
|
| 2005 |
Major DT, York DM, Gao J. Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction. Journal of the American Chemical Society. 127: 16374-5. PMID 16305206 DOI: 10.1021/Ja055881U |
0.581 |
|
| 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 |
0.729 |
|
| 2005 |
Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Physical Chemistry Chemical Physics : Pccp. 7: 3070-9. PMID 16186912 DOI: 10.1039/B504941E |
0.7 |
|
| 2005 |
Gregersen BA, York DM. High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods. The Journal of Chemical Physics. 122: 194110. PMID 16161566 DOI: 10.1063/1.1899146 |
0.778 |
|
| 2005 |
Liu Y, Lopez X, York DM. Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory. Chemical Communications (Cambridge, England). 3909-11. PMID 16075068 DOI: 10.1039/B502568K |
0.359 |
|
| 2005 |
Range K, Mayaan E, Maher LJ, York DM. The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. Nucleic Acids Research. 33: 1257-68. PMID 15741179 DOI: 10.1093/Nar/Gki272 |
0.797 |
|
| 2005 |
López CS, Faza ON, de Lera AR, York DM. Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 2081-93. PMID 15714539 DOI: 10.1002/Chem.200400790 |
0.466 |
|
| 2005 |
López CS, Nieto Faza O, Cossío FP, York DM, de Lera AR. Ellipticity: a convenient tool to characterize electrocyclic reactions. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 1734-8. PMID 15669038 DOI: 10.1002/Chem.200401026 |
0.314 |
|
| 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 |
0.645 |
|
| 2005 |
Nam K, Gao J, York DM. An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations Journal of Chemical Theory and Computation. 1: 2-13. DOI: 10.1021/ct049941i |
0.47 |
|
| 2005 |
Mercero JM, Matxain JM, Lopez X, York DM, Largo A, Eriksson LA, Ugalde JM. Theoretical methods that help understanding the structure and reactivity of gas phase ions International Journal of Mass Spectrometry. 240: 37-99. DOI: 10.1016/J.Ijms.2004.09.018 |
0.323 |
|
| 2004 |
Mayaan E, Range K, York DM. Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 9: 807-17. PMID 15328556 DOI: 10.1007/S00775-004-0583-7 |
0.797 |
|
| 2004 |
López CS, Faza ON, Gregersen BA, Lopez X, de Lera AR, York DM. Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 5: 1045-9. PMID 15298394 DOI: 10.1002/Cphc.200400091 |
0.805 |
|
| 2004 |
Khandogin J, York DM. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. Proteins. 56: 724-37. PMID 15281126 DOI: 10.1002/Prot.20171 |
0.393 |
|
| 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 |
0.683 |
|
| 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 |
0.705 |
|
| 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 |
0.702 |
|
| 2004 |
Gregersen BA, Lopez X, York DM. Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation. Journal of the American Chemical Society. 126: 7504-13. PMID 15198597 DOI: 10.1021/Ja031815L |
0.818 |
|
| 2004 |
Range K, McGrath MJ, Lopez X, York DM. The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution. Journal of the American Chemical Society. 126: 1654-65. PMID 14871095 DOI: 10.1021/Ja0356277 |
0.628 |
|
| 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 |
0.724 |
|
| 2003 |
Khandogin J, Musier-Forsyth K, York DM. Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods. Journal of Molecular Biology. 330: 993-1004. PMID 12860122 DOI: 10.1016/S0022-2836(03)00658-2 |
0.358 |
|
| 2003 |
Gregersen BA, Lopez X, York DM. Hybrid QM/MM study of thio effects in transphosphorylation reactions. Journal of the American Chemical Society. 125: 7178-9. PMID 12797782 DOI: 10.1021/Ja035167H |
0.815 |
|
| 2003 |
Sherer EC, York DM, Cramer CJ. Fast approximate methods for calculating nucleic acid base pair interaction energies. Journal of Computational Chemistry. 24: 57-67. PMID 12483675 DOI: 10.1002/Jcc.10150 |
0.39 |
|
| 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 |
0.716 |
|
| 2003 |
Lopez X, York DM. Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus Theoretical Chemistry Accounts. 109: 149-159. DOI: 10.1007/S00214-002-0422-2 |
0.403 |
|
| 2003 |
Gao J, York D. Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecular mechanical potentials (2001) Theoretical Chemistry Accounts. 109: 99. DOI: 10.1007/S00214-002-0414-2 |
0.548 |
|
| 2002 |
Ayala I, Range K, York D, Barry BA. Spectroscopic properties of tyrosyl radicals in dipeptides. Journal of the American Chemical Society. 124: 5496-505. PMID 11996592 DOI: 10.1021/Ja0164327 |
0.582 |
|
| 2002 |
Khandogin J, York DM. Quantum mechanical characterization of nucleic acids in solution: A linear-scaling study of charge fluctuations in DNA and RNA Journal of Physical Chemistry B. 106: 7693-7703. DOI: 10.1021/Jp0146667 |
0.392 |
|
| 2002 |
Hu A, York DM, Woo TK. Time-dependent density functional theory calculations of molecular static and dynamic polarizabilities, cauchy coefficients and their anisotropies with atomic numerical basis functions Journal of Molecular Structure: Theochem. 591: 255-266. DOI: 10.1016/S0166-1280(02)00246-4 |
0.33 |
|
| 2001 |
Lopez X, York DM, Dejaegere A, Karplus M. Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A International Journal of Quantum Chemistry. 86: 10-26. DOI: 10.1002/Qua.1601 |
0.625 |
|
| 2000 |
Khandogin J, Hu A, York DM. Electronic Structure Properties of Solvated Biomolecules: A Quantum Approach for Macromolecular Characterization Journal of Computational Chemistry. 21: 1562-1571. DOI: 10.1002/1096-987X(200012)21:16<1562::Aid-Jcc13>3.0.Co;2-E |
0.348 |
|
| 1998 |
York DM, Lee TS, Yang W. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods Physical Review Letters. 80: 5011-5014. DOI: 10.1103/Physrevlett.80.5011 |
0.535 |
|
| 1996 |
Lee TS, York DM, Yang W. Linear-scaling semiempirical quantum calculations for macromolecules Journal of Chemical Physics. 105: 2744-2750. DOI: 10.1063/1.472136 |
0.56 |
|
| 1996 |
York DM, Yang W. A chemical potential equalization method for molecular simulations Journal of Chemical Physics. 104: 159-172. DOI: 10.1063/1.470886 |
0.59 |
|
| 1996 |
York DM, Lee TS, Yang W. Quantum mechanical study of aqueous polarization effects on biological macromolecules Journal of the American Chemical Society. 118: 10940-10941. DOI: 10.1021/Ja961937W |
0.49 |
|
| 1996 |
Ni H, York DM, Bartolotti L, Wells RL, Yang W. Density-functional study of the geometries, stabilities, and bond energies of group III-V (13-15) four-membered-ring compounds Journal of the American Chemical Society. 118: 5732-5736. DOI: 10.1021/Ja951706+ |
0.503 |
|
| 1996 |
York DM, Lee TS, Yang W. Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules Chemical Physics Letters. 263: 297-304. DOI: 10.1016/S0009-2614(96)01198-0 |
0.57 |
|
| 1995 |
Lee TS, York DM, Yang W. A new definition of atomic charges based on a variational principle for the electrostatic potential energy The Journal of Chemical Physics. 102: 7549-7556. DOI: 10.1063/1.469086 |
0.573 |
|
| 1995 |
York DM, Yang W, Lee H, Darden T, Pedersen LG. Toward the accurate modeling of DNA: The importance of long-range electrostatics Journal of the American Chemical Society. 117: 5001-5002. DOI: 10.1021/Ja00122A034 |
0.725 |
|
| 1995 |
York DM. A generalized formulation of electronegativity equalization from density-functional theory International Journal of Quantum Chemistry. 56: 385-394. DOI: 10.1002/Qua.560560842 |
0.385 |
|
| 1994 |
York DM, Wlodawer A, Pedersen LG, Darden TA. Atomic-level accuracy in simulations of large protein crystals. Proceedings of the National Academy of Sciences of the United States of America. 91: 8715-8. PMID 7521533 DOI: 10.1073/Pnas.91.18.8715 |
0.661 |
|
| 1994 |
York D, Lu JP, Yang W. Density-functional calculations of the structure and stability of C240 Physical Review B. 49: 8526-8528. DOI: 10.1103/Physrevb.49.8526 |
0.525 |
|
| 1994 |
York D, Yang W. The fast Fourier Poisson method for calculating Ewald sums The Journal of Chemical Physics. 101: 3298-3300. DOI: 10.1063/1.467576 |
0.515 |
|
| 1994 |
York DM, Bartolotti LJ, Darden TA, Pedersen LG, Anderson MW. Simulations of the solution structure of HIV‐1 protease in the presence and absence of bound zinc Journal of Computational Chemistry. 15: 61-71. DOI: 10.1002/Jcc.540150108 |
0.68 |
|
| 1993 |
York DM, Darden TA, Pedersen LG, Anderson MW. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry. 32: 1443-53. PMID 8431424 DOI: 10.1021/Bi00057A007 |
0.659 |
|
| 1993 |
York DM, Darden TA, Pedersen LG, Anderson MW. Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates. Environmental Health Perspectives. 101: 246-50. PMID 8404763 DOI: 10.1289/Ehp.93101246 |
0.661 |
|
| 1993 |
York DM, Darden TA, Pedersen LG. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods The Journal of Chemical Physics. 99: 8345-8348. DOI: 10.1063/1.465608 |
0.668 |
|
| 1993 |
Darden T, York D, Pedersen L. Particle mesh Ewald: AnN⋅log(N) method for Ewald sums in large systems The Journal of Chemical Physics. 98: 10089-10092. DOI: 10.1063/1.464397 |
0.64 |
|
| 1993 |
York DM, Darden TA, Pedersen LG, Anderson MW. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. [Erratum to document cited in CA118(21):208404x] Biochemistry. 32: 3196-3196. DOI: 10.1021/Bi00063A035 |
0.619 |
|
| 1992 |
York DM, Darden T, Deerfield D, Pedersen LG. The interaction of Na(I), Ca(II), and Mg(II) metal ions with duplex DNA: A theoretical modeling study International Journal of Quantum Chemistry. 44: 145-166. DOI: 10.1002/Qua.560440715 |
0.667 |
|
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