Darrin M. York

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

J. Phys. Chem. B, (2019) 123, 4611-4624
DOI: 10.1021/acs.jpcb.8b11923

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

ACS Chem. Biol. , (2019) ,
DOI: https://pubs.acs.org/doi/full/10.1021/acschembio.9b00202

Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

ACS Catal., (2019) 9, 5803-5815
DOI: 10.1021/acscatal.9b01155

Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction

J. Phys. Chem. A, (2019) 123, 3647-3654
DOI: 10.1021/acs.jpca.9b00172

Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory

J. Am. Chem. Soc., (2019) 141, 2435
DOI: 10.1021/jacs.8b11474

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

J. Chem. Inf. Model., (2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Molecules, (2018) 23, 2695-2719
DOI: 10.3390/molecules23102695

On the convergence of multi-scale free energy simulations

Mol Simul, (2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

J. Chem. Theory Comput., (2018) 14, 1564–1582
DOI: 10.1021/acs.jctc.7b01175 Download PDF

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