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Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

(2024) 160, 224104
DOI: 10.1063/5.0211276
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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

(2024) 29, 2703
DOI: 10.3390/molecules29112703
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Alchemical Enhanced Sampling with Optimized Phase Space Overlap

(2024) 20, 3935-3953
DOI: doi.org/10.1021/acs.jctc.4c00251
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Surface-Accelerated String Method for Locating Minimum Free Energy Paths

(2024) 20, 2058–2073
DOI: 10.1021/acs.jctc.3c01401
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AmberTools

(2023) 63, 6183-6191
DOI: 10.1021/acs.jcim.3c01153
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Modern Alchemical Free Energy Methods for Drug Discovery Explained

(2023) 3, 478-491
DOI: 10.1021/acsphyschemau.3c00033
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DeePMD-kit v2: A software package for deep potential models

(2023) 159, 054801
DOI: 10.1063/5.0155600
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Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis

(2023) 62, 2079-2092
DOI: 10.1021/acs.biochem.3c00160
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Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations

(2023) 158, 174105-174115
DOI: 10.1063/5.0147218
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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

(2023) 51, 4508-4518
DOI: 10.1093/nar/gkad260
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Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: conformers, tautomers and protonation states

(2023) 158, 124110
DOI: 10.1063/5.0139281
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Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models

(2023) 19, 1322-1332
DOI: 10.1021/acs.jctc.2c01277
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Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

(2023) 145, 2830-2839
DOI: 10.1021/jacs.2c10079
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Chapter 6 Learning DeePMD-Kit: A Guide to Building Deep Potential Models
In A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

(2023) Chapter: 6 Edited by: Yong Wang and Ruhong Zhou Publishers: AIP Publishing
DOI: 10.1063/9780735425279_006 ISBN: 978-0-7354-2527-9
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QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery

(2023) 19, 1261-1275
DOI: 10.1021/acs.jctc.2c01172
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ACES: Optimized Alchemically Enhanced Sampling

(2023) 19, 472-487
DOI: 10.1021/acs.jctc.2c00697
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AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways

(2023) 19, 640-658
DOI: 10.1021/acs.jctc.2c00725
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AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)

(2022) 62, 6069-6083
DOI: 10.1021/acs.jcim.2c00879
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Multireference Generalization of the Weighted Thermodynamic Perturbation Method

(2022) 126, 8519-8533
DOI: 10.1021/acs.jpca.2c06201
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Give and Take: Narrowing the Gap between Theory and Practice of Peer Instructors over Time

(2022) 99, 3370-3385
DOI: 10.1021/acs.jchemed.2c00170
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RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

(2022) 126, 5982-5990
DOI: 10.1021/acs.jpcb.2c03727
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Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign

(2022) 17, 1924-1936
DOI: 10.1021/acschembio.2c00373
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Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions

(2022) 18, 4304-4317
DOI: 10.1021/acs.jctc.2c00151
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Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

(2022) 20, 6216-6230
DOI: 10.1039/d2ob00234e
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Online Orbital Explorer and BingOrbital Game for Inquiry-Based Activities

(2022) 99, 2135-2142
DOI: 10.1021/acs.jchemed.1c01277
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Inquiry-Based Activities and Games That Engage Students in Learning Atomic Orbitals

(2022) 99, 2175-2181
DOI: 10.1021/acs.jchemed.1c01023
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Free Energy Methods in Drug Discovery—Introduction
In Free Energy Methods in Drug Discovery: Current State and Future Directions

(2021) 1397, 1-38 Chapter: 1 Edited by: Kira Armacost and David Thompson Publishers: ACS Publications
DOI: 10.1021/bk-2021-1397.ch001 ISBN: 9780841298057
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Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
In Free Energy Methods in Drug Discovery: Current State and Future Directions

(2021) 1397, 161-204 Chapter: 7 Edited by: Kira Armacost and David Thompson Publishers: ACS Publications
DOI: 10.1021/bk-2021-1397.ch007 ISBN: 9780841298057
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Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/molecular Mechanical Simulations of Chemical Reactions in Solution

(2021) 17, 6993-7009
DOI: 10.1021/acs.jctc.1c00201
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CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

(2021) 61, 4145-4151
DOI: 10.1021/acs.jcim.1c00747
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Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

(2021) 125, 4216-4232
DOI: 10.1021/acs.jpca.1c00736
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Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor

(2021) 60, 1148-1164
DOI: 10.1021/acs.biochem.1c00064
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Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints

(2021) 17, 1326-1336
DOI: 10.1021/acs.jctc.0c01219
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Beneath the Surface: An Investigation of General Chemistry Students’ Study Skills to Predict Course Outcomes

(2021) 98, 281-292
DOI: 10.1021/acs.jchemed.0c01074
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Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020) 60, 5595-5623
DOI: 10.1021/acs.jcim.0c00613
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Through the Looking CLASS: When Peer Leader Learning Attitudes Are Not What They Seem

(2020) 97, 2078-2090
DOI: 10.1021/acs.jchemed.0c00129
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Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) 16, 5512-5525
DOI: 10.1021/acs.jctc.0c00237
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Validation of Free Energy Methods in AMBER

(2020) 60, 5296-5300
DOI: 10.1021/acs.jcim.0c00285
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Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein−Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

(2020) 5, 4611-4619
DOI: 10.1021/acsomega.9b04233
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

(2020) 12, 193-201
DOI: 10.1038/s41557-019-0391-x
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The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design

(2020) 26, 111-126
DOI: 10.1261/rna.071894.119
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Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

(2019) 9, 10612-10617
DOI: 10.1021/acscatal.9b02035
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Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) 15, 5543-5562
DOI: 10.1021/acs.jctc.9b00401
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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution

(2019) 47, 10282-10295
DOI: 10.1093/nar/gkz773
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Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme

(2019) 25, 1439-1456
DOI: 10.1261/rna.071944.119
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Using AMBER18 for Relative Free Energy Calculations

(2019) 59, 3128-3135
DOI: 10.1021/acs.jcim.9b00105
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An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

(2019) 14, 1068-1076
DOI: 10.1021/acschembio.9b00202
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Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

(2019) 9, 5803-5815
DOI: 10.1021/acscatal.9b01155
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Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

(2019) 123, 4611-4624
DOI: 10.1021/acs.jpcb.8b11923
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Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction

(2019) 123, 3647-3654
DOI: 10.1021/acs.jpca.9b00172
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Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory

(2019) 141, 2435
DOI: 10.1021/jacs.8b11474
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A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

(2018) 23, 2695-2719
DOI: 10.3390/molecules23102695
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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462
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On the convergence of multi-scale free energy simulations

(2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741
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Catalytic Strategies of Nucleolytic Ribozymes

(2018) Session 6, 341-344
DOI: 10.1142/10907
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A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

(2018) 14, 1564-1582
DOI: 10.1021/acs.jctc.7b01175
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Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

(2017) 56, 13392-13395
DOI: 10.1002/anie.201705608
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A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

(2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161
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Quantum mechanical force fields for condensed phase molecular simulations

(2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c
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Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

(2017) 13, 3077-3084
DOI: 10.1021/acs.jctc.7b00102
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Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

(2017) 56, 2985-2994
DOI: 10.1021/acs.biochem.6b01192
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Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

(2016) 72, 1062-1072
DOI: 10.1107/S2059798316012225
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A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

(2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158
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Creation of Academic Social Networks (ASNs) for Effective Online eLearning Communities

(2016) Chapter 9, 109-126
DOI: 10.1021/bk-2016-1217.ch009 ISBN: 9780841231252
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The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

(2016) 30, 533-539
DOI: 10.1007/s10822-016-9920-5
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Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

(2016) 12, 2611-2632
DOI: 10.1021/acs.jctc.6b00198
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VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

(2016) 144, 164115
DOI: 10.1063/1.4946779
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A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

(2016) Chapter 2, 1-32
DOI: 10.4032/9789814613934 ISBN: 9789814613927
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Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation

(2016) 138, 3058-3065
DOI: 10.1021/jacs.5b12061
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Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn2+

(2016) 52, 4462-4465
DOI: 10.1039/C5CC10212J
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An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

(2016) 22, 32-48
DOI: 10.1261/rna.053710.115
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Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

(2015) 143, 234111
DOI: 10.1063/1.4937166
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Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

(2015) 119, 15460-15460
DOI: 10.1021/acs.jpcb.5b10423
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Multiscale methods for computational RNA enzymology

(2015) 553, 335-374
DOI: 10.1016/bs.mie.2014.10.064
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Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

(2015) 11, 451-461
DOI: 10.1021/ct500799g
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Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

(2015) 11, 436-450
DOI: 10.1021/ct5007983
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Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

(2015) 21, 963-974
DOI: 10.1261/rna.047357.114
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Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

(2015) 1854, 1801-1808
DOI: 10.1016/j.bbapap.2015.04.022
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Enzyme transition states from theory and experiment

(2015) 1854, 1727-1728
DOI: 10.1016/j.bbapap.2015.08.006
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Heavy Atom Labeled Nucleotides for Measurement of Kinetic Isotope Effects

(2015) 1854, 1737-1745
DOI: 10.1016/j.bbapap.2015.03.007
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Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

(2015) 1854, 1795-1800
DOI: 10.1016/j.bbapap.2015.02.022.
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Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

(2015) 137, 14705-14715
DOI: 10.1021/jacs.5b08395
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Competitive interaction of monovalent cations with DNA from 3D-RISM

(2015) 43, 8405-8415
DOI: 10.1093/nar/gkv830
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Determination of hepatitis delta virus ribozyme N(–1) nucleobase and functional group specificity using internal competition kinetics

(2015) 483, 12-20
DOI: 10.1016/j.ab.2015.04.024
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Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM

(2015) 21, 1-12
DOI: 10.1261/rna.051466.115
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Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

(2015) 36, 1370-1389
DOI: 10.1002/jcc.23933
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Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ Models Commonly Used in Biomolecular Simulations

(2015) 36, 970-982
DOI: 10.1002/jcc.23881
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Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

(2015) 11, 373-377
DOI: 10.1021/ct500776j
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Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

(2015) 54, 1307-1313
DOI: 10.1021/bi5012833
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Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

(2014) 20, 1-9
DOI: 10.1002/chem.201403862
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Recent advances toward a general purpose linear-scaling quantum force field

(2014) 47, 2812-2820
DOI: 10.1021/ar500103g
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Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations

(2014) 16, 15846-15855
DOI: 10.1039/c4cp01050g
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Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

(2014) 21, 96-102
DOI: 10.1016/j.cbpa.2014.06.010.
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Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models

(2014) 35, 1302-1316
DOI: 10.1002/jcc.23628
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Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

(2014) 10, 2246-2254
DOI: 10.1021/ct500205z
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Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

(2014) 136, 7789-7792
DOI: 10.1021/ja500180q
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Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

(2014) 10, 1538-1545
DOI: 10.1021/ct401013s
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Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

(2014) 10, 1086-1098
DOI: 10.1021/ct401035t
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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) 10, 1341-1352
DOI: 10.1021/ct401042b
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Ion counting from explicit solvent simulations and 3D-RISM

(2014) 106, 883-894
DOI: 10.1016/j.bpj.2014.01.021
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Quantum mechanical study of solvent effects in prototype SN2 reactions in solution: Cl- attack on CH3Cl

(2014) 140, 054109
DOI: 10.1063/1.4863344
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Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

(2014) 10, 24-34
DOI: 10.1021/ct400691f
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Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

(2013) 120, 25-91
DOI: 10.1016/B978-0-12-381286-5.00002-0
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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

(2013) 110, 13002-13007
DOI: 10.1073/pnas.1215086110
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A Framework for Flexible and Scalable Replica-Exchange on Production Distributed Cyberinfrastructure.

(2013)
DOI: 10.1145/2484762.2484830
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A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) 9, 1417-1427
DOI: 10.1021/ct3010134
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Molecular Simulations of RNA 2'-O-Transesterification Reaction Models in Solution

(2013) 117, 94-103
DOI: 10.1021/jp3084277
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A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2013) 9, 153-164
DOI: 10.1021/ct300703z
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Exact Relation between Potential of Mean Force and Free-Energy Profile

(2012) 8, 3998-4003
DOI: 10.1021/ct300392f
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Mapping L1 ligase ribozyme conformational switch

(2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035
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Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) 116, 9131-9141
DOI: 10.1021/jp306239c
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Density-functional expansion methods: Grand challenges

(2012) 131, 1145-1161
DOI: 10.1007/s00214-012-1145-7
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Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

(2012) 51, 647-651
DOI: 10.1002/anie.201104147
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Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

(2011) 2, 2538-2543
DOI: 10.1021/jz201106y
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Density-functional expansion methods: Generalization of the auxiliary basis

(2011) 134, 194103
DOI: 10.1063/1.3587052
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Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts

(2011) 39, 3988-4006
DOI: 10.1093/nar/gkq1341
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Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

(2011) 7, 1-3
DOI: 10.1021/ct100467t
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Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis

(2010) 114, 13911-13921
DOI: 10.1021/jp107450n
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Computational mutagenesis studies of hammerhead ribozyme catalysis

(2010) 132, 13505-13518
DOI: 10.1021/ja105956u
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Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations
In Annual Reports in Computational Chemistry

(2010) 6, 168-200
DOI: 10.1016/S1574-1400(10)06001-9 ISBN: 978-0-44-453552-8
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Molecular dynamics simulation of bovine pancreatic ribonuclease A - CpA and transition state-like complexes

(2010) 114, 7371-7382
DOI: 10.1021/jp909004y
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Identification of dynamical hinge points of the L1 ligase molecular switch

(2010) 16, 769-780
DOI: 10.1261/rna.1897810
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Exocyclic deoxyadenosine adducts of 1,2,3,4-Diepoxybutane: Synthesis, structural elucidation, and mechanistic studies

(2010) 23, 118-133
DOI: 10.1021/tx900312e
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CHARMM: The biomolecular simulation program

(2009) 30, 1545-1614
DOI: 10.1002/jcc.21287
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Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations

(2009) 7, 377-408 Chapter: Multi-scale Quantum Models for Biocatalysis
DOI: 10.1007/978-1-4020-9956-4_14 ISBN: 978-1-4020-9956-4
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Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

(2009) 388, 195-206
DOI: 10.1016/j.jmb.2009.02.054
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Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

(2009) 122, 179-188
DOI: 10.1007/s00214-008-0497-5
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Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory. 1. Parameterization

(2008) 4, 2067-2084
DOI: 10.1021/ct800330d
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Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

(2008) 29, 1895-1904
DOI: 10.1002/jcc.20946
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Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

(2008) 14, 1501-1507
DOI: 10.1261/rna.863108
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Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables

(2008) 129, 016102
DOI: 10.1063/1.2945897
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Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

(2008) 130, 7168-7169
DOI: 10.1021/ja711242b
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Contracted auxiliary Gaussian basis integral and derivative evaluation

(2008) 128, 064104
DOI: 10.1063/1.2821745
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Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

(2008) 130, 4680-4691
DOI: 10.1021/ja0759141
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Solvent structure and hammerhead ribozyme catalysis

(2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010
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Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

(2008) 130, 3053-3064
DOI: 10.1021/ja076529e
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New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution

(2007) 201-218 Chapter: Multiscale Simulation Methods for Nanomaterials
DOI: 10.1002/9780470191675.ch12 ISBN: 9780470191675
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Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

(2007) 127, 194101
DOI: 10.1063/1.2778428
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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

(2007) 111, 10861-10873
DOI: 10.1021/jp074167r
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Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

(2007) 3, 325-327
DOI: 10.1021/ct6003142
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Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

(2007) 3, 486-504
DOI: 10.1021/ct6002466
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CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

(2007) 28, 495-507
DOI: 10.1002/jcc.20474
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Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

(2006) 110, 24708-24719
DOI: 10.1021/jp066263i
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Simulations of phosphoryl transfer reactions using multi-scale quantum models

(2006) 181-192
DOI: 10.1039/9781847555373
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QCRNA 1.0: A database of quantum calculations for RNA catalysis

(2006) 25, 423-433
DOI: 10.1016/j.jmgm.2006.02.011
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Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

(2006) 45, 10043-10053
DOI: 10.1021/bi060869f
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Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

(2006) 110, 11525-11539
DOI: 10.1021/jp0603942
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Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

(2006) 110, 10970-10981
DOI: 10.1021/jp061503f
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Multi-level and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

(2006) 110, 791-797
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A charge-scaling implementation of the variational electrostatic projection method

(2006) 27, 103-115
DOI: 10.1002/jcc.20318
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Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction

(2005) 127, 16374-16375
DOI: 10.1021/ja055881u
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A semiempirical quantum model for hydrogen bonded nucleic acid base pairs

(2005) 1, 1275-1285
DOI: 10.1021/ct050102l
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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

(2005) 109, 19987-20003
DOI: 10.1021/jp053146z
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Improvement of semiempirical response properties with charge-dependent response density

(2005) 123, 164108
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Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions

(2005) 109, 13827-13834
DOI: 10.1021/jp051042i
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Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

(2005) 7, 3070-3079
DOI: 10.1039/B504941E
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Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

(2005) 109, 9799-9809
DOI: 10.1021/jp044062d
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Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

(2005) 109, 9810-9817
DOI: 10.1021/jp044061l
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High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

(2005) 122, 194110
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Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

(2005) 11, 2081-2093
DOI: 10.1002/chem.200400790
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Ellipticity: a convenient tool to characterize electrocyclic reactions

(2005) 11, 1734-1738
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The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

(2005) 33, 1257-1268
DOI: 10.1093/nar/gki272
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Variational Electrostatic Projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

(2005) 109, 536-556
DOI: 10.1021/jp0469968
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An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

(2005) 1, 2-13
DOI: 10.1021/ct049941i
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Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

(2005) 31, 3909-3911
DOI: 10.1039/B502568K
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Theoretical methods that help understanding the structure and reactivity of gas phase ions

(2005) 240, 37-99
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Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

(2004) 9, 807-817
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Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

(2004) 56, 724-737
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Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

(2004) 5, 1045-1049
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Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

(2004) 126, 7504-7513
DOI: 10.1021/ja031815l
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Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

(2004) 120, 9903-9906
DOI: 10.1063/1.1756583
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Theoretical Study of the Vinyl Allene Oxide to Cyclopent-2-en-1-one Rearrangement:? Mechanism, Torquoselectivity and Solvent Effects

(2004) 69, 3635-3644
DOI: 10.1021/jo049620z
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Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

(2004) 120, 7939
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The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

(2004) 126, 1654-1665
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Design and application of a multicoefficient correlatiomethod for dispersion interactions

(2004) 120, 590
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High-level ab initio methods for calculation of accurate potential energy surfaces of van der Waals complexes

(2004) 98, 388-408
DOI: 10.1002/qua.20074
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Examination of the correlation energy and second virial coefficients from accurate ab initio calculations of rare-gas dimers

(2003) 119, 2618-2622
DOI: 10.1063/1.1587684
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Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

(2003) 330, 993-1004
DOI: 10.1016/S0022-2836(03)00658-2
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Hybrid QM/MM study of thio effects in transphosphorylation reactions

(2003) 125, 7178-7179
DOI: 10.1021/ja035167h
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Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

(2003) 109, 149-159
DOI: 10.1007/s00214-002-0422-2
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Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecularmechanical potentials (2001)

(2003) 109, 99
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Fast approximate methods for calculating nucleic acid base pair interaction energies

(2003) 24, 57-67
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Time-dependent density functional theory calculations of molecular static and dynamic polarizabilities, cauchy coefficients and their anisotropies with atomic numerical basis functions

(2002) 591, 255-266
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Quantum Mechanical Characterization of Nucleic Acids in Solution:? A Linear-Scaling Study of Charge Fluctuations in DNA and RNA

(2002) 106, 7693-7703
DOI: 10.1021/jp0146667
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Spectroscopic Properties of Tyrosyl Radicals in Dipeptides

(2002) 124, 5496-5505
DOI: 10.1021/ja0164327
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Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A

(2002) 86, 10-26
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Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization

(2000) 21, 1562-1571
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A Smooth Solvation Potential Based on the Conductor-Like Screening Model

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Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution

(1998) 712, 275-287
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Quantum Mechanical Treatment of Biological Macromolecules in Solution using Linear-Scaling Electronic Structure Methods

(1998) 80, 5011-5014
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Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

(1996) 263, 297-304
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Density-Functional Study of the Geometries, Stabilities, and Bond Energies of Group III-V (13-15) Four-Membered-Ring Compounds

(1996) 118, 5732-5736
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Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules

(1996) 118, 10940-10941
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Linear-scaling semiempirical quantum calculations for macromolecules

(1996) 105, 2744
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A chemical potential equalization method for molecular simulations

(1996) 104, 159-172
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A new definition of atomic charges based on a variational principle for the electrostatic potential energy

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Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

(1995) 117, 5001-5002
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The effect of hydrostatic pressure on protein crystals investigated by molecular simulation

(1995) 27, 203-215
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A generalized formulation of electronegativity equalization from density-functional theory

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The Fast Fourier Poisson Method for Calculating Ewald Sums

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Atomic-level Accuracy in Simulations of Large Protein Crystals

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Density-functional Calculations of the Structure and Stability of C240

(1994) 49, 8526-8528
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Simulations of the Solution Structure of the HIV-1 Protease in the Presence and Absence of Bound Zinc

(1994) 15, 61-71
DOI: 10.1002/jcc.540150108
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The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: A Comparison of the Ewald and Truncated List Methods

(1993) 99, 8345
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Molecular Modeling Studies Suggest that Zinc Ions Inhibit HIV-1 Protease by Binding at Catalytic Aspartates

(1993) 101, 246-250
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Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems

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Molecular Dynamics Simulation of HIV-1 Protease in a Crystalline Environment and in Solution

(1993) 32, 1443-1453
DOI: 10.1021/bi00057a007
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The Interaction of Na(I), Ca(II), and Mg(II) Metal Ions with Duplex DNA: A Theoretical Modeling Study

(1992) 44, 145-166
DOI: 10.1002/qua.560440715
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