Filters
From: To:
-



Surface-Accelerated String Method for Locating Minimum Free Energy Paths

(2024)
DOI: 10.1021/acs.jctc.3c01401
Read More View Full Article
AmberTools

(2023) 63, 6183-6191
DOI: 10.1021/acs.jcim.3c01153
Read More View Full Article Download PDF
Modern Alchemical Free Energy Methods for Drug Discovery Explained

(2023) 3, 478-491
DOI: 10.1021/acsphyschemau.3c00033
Read More View Full Article Download PDF
DeePMD-kit v2: A software package for deep potential models

(2023) 159, 054801
DOI: 10.1063/5.0155600
Read More View Full Article Download PDF
Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis

(2023) 62, 2079-2092
DOI: 10.1021/acs.biochem.3c00160
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

(2023) 51, 4508-4518
DOI: 10.1093/nar/gkad260
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models

(2023) 19, 1322-1332
DOI: 10.1021/acs.jctc.2c01277
Read More View Full Article Download PDF
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

(2023) 145, 2830-2839
DOI: 10.1021/jacs.2c10079
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery

(2023) 19, 1261-1275
DOI: 10.1021/acs.jctc.2c01172
Read More View Full Article Download PDF
ACES: Optimized Alchemically Enhanced Sampling

(2023) 19, 472-487
DOI: 10.1021/acs.jctc.2c00697
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Multireference Generalization of the Weighted Thermodynamic Perturbation Method

(2022) 126, 8519-8533
DOI: 10.1021/acs.jpca.2c06201
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

(2022) 126, 5982-5990
DOI: 10.1021/acs.jpcb.2c03727
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Online Orbital Explorer and BingOrbital Game for Inquiry-Based Activities

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

(2022) 99, 2175-2181
DOI: 10.1021/acs.jchemed.1c01023
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article
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
Read More View Full Article Download PDF
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

(2021) 61, 4145-4151
DOI: 10.1021/acs.jcim.1c00747
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

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

(2020) 97, 2078-2090
DOI: 10.1021/acs.jchemed.0c00129
Read More View Full Article Download PDF
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) 16, 5512-5525
DOI: 10.1021/acs.jctc.0c00237
Read More View Full Article Download PDF
Validation of Free Energy Methods in AMBER

(2020) 60, 5296-5300
DOI: 10.1021/acs.jcim.0c00285
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Using AMBER18 for Relative Free Energy Calculations

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

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

(2019) 9, 5803-5815
DOI: 10.1021/acscatal.9b01155
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction

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

(2019) 141, 2435
DOI: 10.1021/jacs.8b11474
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
On the convergence of multi-scale free energy simulations

(2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741
Read More View Full Article Download PDF
Catalytic Strategies of Nucleolytic Ribozymes

(2018) Session 6, 341-344
DOI: 10.1142/10907
Read More View Full Article Download PDF
A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

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

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

(2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161
Read More View Full Article Download PDF
Quantum mechanical force fields for condensed phase molecular simulations

(2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

(2016) 72, 1062-1072
DOI: 10.1107/S2059798316012225
Read More View Full Article Download PDF
A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

(2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

(2016) 144, 164115
DOI: 10.1063/1.4946779
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

(2015) 143, 234111
DOI: 10.1063/1.4937166
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Multiscale methods for computational RNA enzymology

(2015) 553, 335-374
DOI: 10.1016/bs.mie.2014.10.064
Read More View Full Article Download PDF
Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

(2015) 11, 451-461
DOI: 10.1021/ct500799g
Read More View Full Article Download PDF
Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

(2015) 11, 436-450
DOI: 10.1021/ct5007983
Read More View Full Article Download PDF
Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

(2015) 21, 963-974
DOI: 10.1261/rna.047357.114
Read More View Full Article Download PDF
Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

(2015) 1854, 1801-1808
DOI: 10.1016/j.bbapap.2015.04.022
Read More View Full Article Download PDF
Enzyme transition states from theory and experiment

(2015) 1854, 1727-1728
DOI: 10.1016/j.bbapap.2015.08.006
Read More View Full Article Download PDF
Heavy Atom Labeled Nucleotides for Measurement of Kinetic Isotope Effects

(2015) 1854, 1737-1745
DOI: 10.1016/j.bbapap.2015.03.007
Read More View Full Article Download PDF
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.
Read More View Full Article Download PDF
Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

(2015) 137, 14705-14715
DOI: 10.1021/jacs.5b08395
Read More View Full Article Download PDF
Competitive interaction of monovalent cations with DNA from 3D-RISM

(2015) 43, 8405-8415
DOI: 10.1093/nar/gkv830
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

(2015) 36, 1370-1389
DOI: 10.1002/jcc.23933
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

(2015) 54, 1307-1313
DOI: 10.1021/bi5012833
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Recent advances toward a general purpose linear-scaling quantum force field

(2014) 47, 2812-2820
DOI: 10.1021/ar500103g
Read More View Full Article Download PDF
Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations

(2014) 16, 15846-15855
DOI: 10.1039/c4cp01050g
Read More View Full Article Download PDF
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.
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

(2014) 10, 2246-2254
DOI: 10.1021/ct500205z
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

(2014) 10, 1538-1545
DOI: 10.1021/ct401013s
Read More View Full Article Download PDF
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

(2014) 10, 1086-1098
DOI: 10.1021/ct401035t
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Ion counting from explicit solvent simulations and 3D-RISM

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

(2014) 140, 054109
DOI: 10.1063/1.4863344
Read More View Full Article Download PDF
Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

(2014) 10, 24-34
DOI: 10.1021/ct400691f
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
A Framework for Flexible and Scalable Replica-Exchange on Production Distributed Cyberinfrastructure.

(2013)
DOI: 10.1145/2484762.2484830
Read More View Full Article Download PDF
A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) 9, 1417-1427
DOI: 10.1021/ct3010134
Read More View Full Article Download PDF
Molecular Simulations of RNA 2'-O-Transesterification Reaction Models in Solution

(2013) 117, 94-103
DOI: 10.1021/jp3084277
Read More View Full Article Download PDF
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2013) 9, 153-164
DOI: 10.1021/ct300703z
Read More View Full Article Download PDF
Exact Relation between Potential of Mean Force and Free-Energy Profile

(2012) 8, 3998-4003
DOI: 10.1021/ct300392f
Read More View Full Article Download PDF
Mapping L1 ligase ribozyme conformational switch

(2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035
Read More View Full Article Download PDF
Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) 116, 9131-9141
DOI: 10.1021/jp306239c
Read More View Full Article Download PDF
Density-functional expansion methods: Grand challenges

(2012) 131, 1145-1161
DOI: 10.1007/s00214-012-1145-7
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Density-functional expansion methods: Generalization of the auxiliary basis

(2011) 134, 194103
DOI: 10.1063/1.3587052
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis

(2010) 114, 13911-13921
DOI: 10.1021/jp107450n
Read More View Full Article Download PDF
Computational mutagenesis studies of hammerhead ribozyme catalysis

(2010) 132, 13505-13518
DOI: 10.1021/ja105956u
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Molecular dynamics simulation of bovine pancreatic ribonuclease A - CpA and transition state-like complexes

(2010) 114, 7371-7382
DOI: 10.1021/jp909004y
Read More View Full Article Download PDF
Identification of dynamical hinge points of the L1 ligase molecular switch

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

(2010) 23, 118-133
DOI: 10.1021/tx900312e
Read More View Full Article Download PDF
CHARMM: The biomolecular simulation program

(2009) 30, 1545-1614
DOI: 10.1002/jcc.21287
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Contracted auxiliary Gaussian basis integral and derivative evaluation

(2008) 128, 064104
DOI: 10.1063/1.2821745
Read More View Full Article Download PDF
Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

(2008) 130, 4680-4691
DOI: 10.1021/ja0759141
Read More View Full Article Download PDF
Solvent structure and hammerhead ribozyme catalysis

(2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010
Read More View Full Article Download PDF
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

(2008) 130, 3053-3064
DOI: 10.1021/ja076529e
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

(2007) 127, 194101
DOI: 10.1063/1.2778428
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

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

(2006) 110, 24708-24719
DOI: 10.1021/jp066263i
Read More View Full Article Download PDF
Simulations of phosphoryl transfer reactions using multi-scale quantum models

(2006) 181-192
DOI: 10.1039/9781847555373
Read More View Full Article Download PDF
QCRNA 1.0: A database of quantum calculations for RNA catalysis

(2006) 25, 423-433
DOI: 10.1016/j.jmgm.2006.02.011
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

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

(2006) 110, 791-797
DOI: 10.1021/jp054360q
Read More View Full Article Download PDF
A charge-scaling implementation of the variational electrostatic projection method

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

(2005) 127, 16374-16375
DOI: 10.1021/ja055881u
Read More View Full Article Download PDF
A semiempirical quantum model for hydrogen bonded nucleic acid base pairs

(2005) 1, 1275-1285
DOI: 10.1021/ct050102l
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Improvement of semiempirical response properties with charge-dependent response density

(2005) 123, 164108
DOI: 10.1063/1.2080007
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

(2005) 109, 9799-9809
DOI: 10.1021/jp044062d
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

(2005) 122, 194110
DOI: 10.1063/1.1899146
Read More View Full Article Download PDF
Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

(2005) 11, 2081-2093
DOI: 10.1002/chem.200400790
Read More View Full Article Download PDF
Ellipticity: a convenient tool to characterize electrocyclic reactions

(2005) 11, 1734-1738
DOI: 10.1002/chem.200401026
Read More View Full Article Download PDF
The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

(2005) 33, 1257-1268
DOI: 10.1093/nar/gki272
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

(2005) 1, 2-13
DOI: 10.1021/ct049941i
Read More View Full Article Download PDF
Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

(2005) 31, 3909-3911
DOI: 10.1039/B502568K
Read More View Full Article Download PDF
Theoretical methods that help understanding the structure and reactivity of gas phase ions

(2005) 240, 37-99
DOI: 10.1016/j.ijms.2004.09.018
Read More View Full Article Download PDF
Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

(2004) 9, 807-817
DOI: 10.1007/s00775-004-0608-2
Read More View Full Article Download PDF
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

(2004) 56, 724-737
DOI: 10.1002/prot.20171
Read More View Full Article Download PDF
Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

(2004) 5, 1045-1049
DOI: 10.1002/cphc.200400091
Read More View Full Article Download PDF
Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

(2004) 126, 7504-7513
DOI: 10.1021/ja031815l
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
DOI: 10.1063/1.1690232
Read More View Full Article Download PDF
The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

(2004) 126, 1654-1665
DOI: 10.1021/ja0356277
Read More View Full Article Download PDF
Design and application of a multicoefficient correlatiomethod for dispersion interactions

(2004) 120, 590
DOI: 10.1063/1.1630955
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Hybrid QM/MM study of thio effects in transphosphorylation reactions

(2003) 125, 7178-7179
DOI: 10.1021/ja035167h
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecularmechanical potentials (2001)

(2003) 109, 99
DOI: 10.1007/s00214-002-0414-2
Read More View Full Article Download PDF
Fast approximate methods for calculating nucleic acid base pair interaction energies

(2003) 24, 57-67
DOI: 10.1002/jcc.10150
Read More View Full Article Download PDF
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
DOI: 10.1016/S0166-1280(02)00246-4
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
Spectroscopic Properties of Tyrosyl Radicals in Dipeptides

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

(2002) 86, 10-26
DOI: 10.1002/qua.1601
Read More View Full Article Download PDF
Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization

(2000) 21, 1562-1571
DOI: 10.1002/1096-987X(200012)21:16<1562::AID-JCC13>3.0.CO;2-E
Read More View Full Article Download PDF
A Smooth Solvation Potential Based on the Conductor-Like Screening Model

(1999) 103, 11060-11079
DOI: 10.1021/jp992097l
Read More View Full Article Download PDF
Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution

(1998) 712, 275-287
DOI: 10.1021/bk-1998-0712.ch018
Read More View Full Article Download PDF
Quantum Mechanical Treatment of Biological Macromolecules in Solution using Linear-Scaling Electronic Structure Methods

(1998) 80, 5011-5014
DOI: 10.1103/PhysRevLett.80.5011
Read More View Full Article Download PDF
Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

(1996) 263, 297-304
DOI: 10.1016/S0009-2614(96)01198-0
Read More View Full Article Download PDF
Density-Functional Study of the Geometries, Stabilities, and Bond Energies of Group III-V (13-15) Four-Membered-Ring Compounds

(1996) 118, 5732-5736
DOI: 10.1021/ja951706+
Read More View Full Article Download PDF
Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules

(1996) 118, 10940-10941
DOI: 10.1021/ja961937w
Read More View Full Article Download PDF
Linear-scaling semiempirical quantum calculations for macromolecules

(1996) 105, 2744
DOI: 10.1063/1.472136
Read More View Full Article Download PDF
A chemical potential equalization method for molecular simulations

(1996) 104, 159-172
DOI: 10.1063/1.470886
Read More View Full Article Download PDF
A new definition of atomic charges based on a variational principle for the electrostatic potential energy

(1995) 102, 7549
DOI: 10.1063/1.469086
Read More View Full Article Download PDF
Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

(1995) 117, 5001-5002
DOI: 10.1021/ja00122a034
Read More View Full Article Download PDF
The effect of hydrostatic pressure on protein crystals investigated by molecular simulation

(1995) 27, 203-215
DOI: 10.1007/978-94-011-0497-5_17
Read More View Full Article Download PDF
A generalized formulation of electronegativity equalization from density-functional theory

(1995) 56, 385-394
DOI: 10.1002/qua.560560842
Read More View Full Article Download PDF
The Fast Fourier Poisson Method for Calculating Ewald Sums

(1994) 101, 3298
DOI: 10.1063/1.467576
Read More View Full Article Download PDF
Atomic-level Accuracy in Simulations of Large Protein Crystals

(1994) 91, 8715-8718
DOI: 10.1073/pnas.91.18.8715
Read More View Full Article Download PDF
Density-functional Calculations of the Structure and Stability of C240

(1994) 49, 8526-8528
DOI: 10.1103/PhysRevB.49.8526
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF
The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: A Comparison of the Ewald and Truncated List Methods

(1993) 99, 8345
DOI: 10.1063/1.465608
Read More View Full Article Download PDF
Molecular Modeling Studies Suggest that Zinc Ions Inhibit HIV-1 Protease by Binding at Catalytic Aspartates

(1993) 101, 246-250
DOI: 10.1289/ehp.93101246
Read More View Full Article Download PDF
Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems

(1993) 98, 10089
DOI: 10.1063/1.464397
Read More View Full Article Download PDF
Molecular Dynamics Simulation of HIV-1 Protease in a Crystalline Environment and in Solution

(1993) 32, 1443-1453
DOI: 10.1021/bi00057a007
Read More View Full Article Download PDF
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
Read More View Full Article Download PDF