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An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

ACS chemical biology, 2019-06, Vol.14 (6), p.1068-1076

2019

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

The Journal of chemical physics, 2024-06, Vol.160 (22)

2024

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Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

Journal of the American Chemical Society, 2023-02, Vol.145 (5), p.2830-2839

2023

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The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme

ACS catalysis, 2024-10, Vol.14 (20), p.15294-15305

2024

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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, 2021-11, Vol.17 (11), p.6993-7009

2021

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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

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2021-05, Vol.125 (19), p.4216-4232

2021

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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

Journal of chemical theory and computation, 2022-07, Vol.18 (7), p.4304-4317

2022

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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution

Nucleic acids research, 2019-11, Vol.47 (19), p.10282-10295

2019

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RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

The journal of physical chemistry. B, 2022-08, Vol.126 (32), p.5982-5990

2022

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Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

Organic & biomolecular chemistry, 2022-08, Vol.20 (31), p.6219-6230

2022

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Software Infrastructure for Next-Generation QM/MM−ΔMLP Force Fields

The journal of physical chemistry. B, 2024-07, Vol.128 (26), p.6257-6271

2024

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Surface-Accelerated String Method for Locating Minimum Free Energy Paths

Journal of chemical theory and computation, 2024-03, Vol.20 (5), p.2058-2073

2024

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Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

The journal of physical chemistry. B, 2019-06, Vol.123 (22), p.4611-4624

2019

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Exchange potentials for semi-classical electrons

Physical chemistry chemical physics : PCCP, 2016-11, Vol.18 (44), p.3748-3753

2016

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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

Nucleic acids research, 2023-05, Vol.51 (9), p.4508-4518

2023

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Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences, 2015-09, Vol.471 (2181), p.20150370

2015

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MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W249-W255

2013

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Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences, 2015-09, Vol.471 (2181), p.1-10

2015

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Transferable pseudoclassical electrons for aufbau of atomic ions

Journal of computational chemistry, 2014-06, Vol.35 (15), p.1159-1164

2014

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Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons

The journal of physical chemistry. B, 2016-07, Vol.120 (26), p.6264-6269

2016

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Transferable Pseudo-Classical Electrons for Aufbau of Atomic Ions

Journal of computational chemistry, 2014-04, Vol.35 (15), p.1159-1164

2014

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Reactive Force Fields with Pseudo-Classical Electrons

Ekesan, Solen

2015

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An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

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

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions

Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

Software Infrastructure for Next-Generation QM/MM−ΔMLP Force Fields

Surface-Accelerated String Method for Locating Minimum Free Energy Paths

Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

Exchange potentials for semi-classical electrons

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues

Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

Transferable pseudoclassical electrons for aufbau of atomic ions

Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons

Transferable Pseudo-Classical Electrons for Aufbau of Atomic Ions

Reactive Force Fields with Pseudo-Classical Electrons

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