List of works - Darrin M York

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

scientific article published on 19 October 2018

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

scientific article published on 22 January 2018

A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations

scientific article

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

scientific article published on 12 December 2012

A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs

scientific article published in November 2005

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

scientific article (publication date: 2016)

A charge-scaling implementation of the variational electrostatic projection method

scientific article published on 01 January 2006

A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields

scientific article published on March 2013

Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models

scientific article

Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

scientific article

Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme

scientific article

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

scientific article published on 16 September 2020

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

scientific article published on 12 July 2014

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

scientific article published on 12 May 2016

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

scientific article published in January 2005

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

scientific article published on 07 June 2019

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

scientific article

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

scientific article

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

scientific article published on 7 July 2005

Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis

scientific article published on January 2013

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

scientific article

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

scientific article

Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

scientific article published on 30 October 2015

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

scientific article published on October 2011

Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment

scientific article

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

scientific article published on February 2015

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

scientific article

Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations

scientific article published on 01 November 2007

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

scientific article published on 22 May 2019

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

scientific article published on 16 June 2022

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations

scientific article published on 4 March 2015

Competitive interaction of monovalent cations with DNA from 3D-RISM.

scientific article published on 24 August 2015

Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

scientific article published on 01 May 2004

Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis ⬇️

scientific article published on September 29, 2010

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

scientific article published on 20 January 2020

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

scientific article published on 05 February 2014

Contracted auxiliary Gaussian basis integral and derivative evaluation

scientific article published on February 2008

DeePMD-kit v2: A software package for deep potential models

scientific article published on 01 August 2023

Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine

scientific article published on March 2009

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

scientific article published on 01 October 2005

Density-functional expansion methods: Grand challenges

scientific article

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations

scientific article

Density-functional expansion methods: generalization of the auxiliary basis

scientific article

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

scientific article published on January 2008

Design and application of a multicoefficient correlation method for dispersion interactions

scientific article published in January 2004

Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics

scientific article published on May 2015

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

scholarly article by Jinzhe Zeng et al published 9 November 2021 in Journal of Chemical Theory and Computation

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods

scientific article published on 17 September 2019

Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

scientific article published on 22 May 2017

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

scientific article published on 01 November 2019

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

scientific article published on 23 March 2015

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

scientific article published on 19 June 2008

Ellipticity: a convenient tool to characterize electrocyclic reactions

scientific article published on 01 March 2005

Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

scientific article published on 01 December 2006

Enzyme transition states from theory and experiment

scientific article published on 21 August 2015

Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

scientific article published on 27 October 2019

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

scientific article

Exact Relation between Potential of Mean Force and Free-Energy Profile

scientific article published on 6 September 2012

Exocyclic deoxyadenosine adducts of 1,2,3,4-diepoxybutane: synthesis, structural elucidation, and mechanistic studies

scientific article

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

scientific article published on 22 July 2013

Extended polarization in third-order SCC-DFTB from chemical-potential equalization

scientific article published on 4 September 2012

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

scientific article published on September 2008

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

scientific article published on 3 October 2007

Fast approximate methods for calculating nucleic acid base pair interaction energies

scientific article published in January 2003

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

scientific article published on 25 February 2020

Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids

scientific article published on 19 November 2015

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

scientific article published on 03 May 2019

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

scientific article published on 25 September 2018

Heavy atom labeled nucleotides for measurement of kinetic isotope effects

scientific article

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

scientific article published in May 2005

Hybrid QM/MM study of thio effects in transphosphorylation reactions

scientific article

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

scientific article

Identification of dynamical hinge points of the L1 ligase molecular switch

scientific article

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

scientific article published on 16 July 2020

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

scientific article

Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

scientific article published on 03 March 2014

Improvement of semiempirical response properties with charge-dependent response density

scientific article published on 01 October 2005

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA.

scientific article

Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation

scientific article published on March 2007

Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

scientific article

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

scientific article published on 29 April 2015

Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations

scientific article published on 6 February 2015

Ion counting from explicit-solvent simulations and 3D-RISM.

scientific article published on February 2014

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+).

scientific article published on 9 February 2016

Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation

scientific article published on 5 September 2017

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

scientific article published on 06 July 2005

Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations

scientific article

Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

scientific article published on 01 June 2004

Mapping L1 ligase ribozyme conformational switch.

scientific article

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions.

scientific article published on 15 September 2014

Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

scientific article

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

scientific article published on 06 March 2023

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

scientific article

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes

scientific article

Molecular simulations of RNA 2'-O-transesterification reaction models in solution

scientific article published on 24 December 2012

Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme

scientific article published on 30 July 2019

Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

scientific article published on 01 January 2006

Multipolar Ewald methods, 1: theory, accuracy, and performance

scientific article

Multipolar Ewald methods, 2: applications using a quantum mechanical force field

scientific article

Multiscale methods for computational RNA enzymology.

scientific article published on 22 January 2015

Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

scientific article published on 01 June 2006

Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

scientific article published on 06 May 2015

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

scientific article published on 01 June 2006

On the convergence of multi-scale free energy simulations

scientific article published on 30 May 2018

Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations

scientific article published on 14 May 2008

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

scientific article published on 11 February 2014

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory

scientific article published on 29 January 2019

Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecularmechanical potentials (2001)

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

scientific article published on 01 March 2005

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

scientific article published on 01 July 2004

Publisher's Note: “Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl− attack on CH3Cl” [].

scientific article published on 4 March 2014

QCRNA 1.0: a database of quantum calculations for RNA catalysis

scientific article published on 3 April 2006

QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery

scientific article published on 25 January 2023

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

scientific article published on 22 April 2019

Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

scientific article published on 01 September 2004

Quantum mechanical force fields for condensed phase molecular simulations

scientific article published on 17 August 2017

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

scientific article published on February 2014

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

scientific article published on 18 March 2008

Recent advances toward a general purpose linear-scaling quantum force field

scientific article

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

scientific article published on 09 February 2016

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach

scientific article published on January 2014

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

scientific article published on 14 February 2008

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

scientific article published in May 2005

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

scientific article published in May 2005

Solvent Structure and Hammerhead Ribozyme Catalysis

scientific article

Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction.

scientific article

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

scientific article published on March 2007

Spectroscopic properties of tyrosyl radicals in dipeptides

scientific article

Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tables

scientific article published on July 2008

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

scientific article published on 24 March 2015

Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

scientific article published on 20 August 2004

The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design

scientific article published on 27 November 2019

The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

scientific article

The fast Fourier Poisson method for calculating Ewald sums

scientific article

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

scientific article published in August 2016

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

scientific article published on 01 February 2004

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

scientific article published on 01 July 2005

Theoretical study of the vinyl allene oxide to cyclopent-2-en-1-one rearrangement: mechanism, torquoselectivity and solvent effects

scientific article

Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

scientific article published on 02 March 2009

Through the Looking CLASS: When Peer Leader Learning Attitudes Are Not What They Seem

scientific article published on 28 July 2020

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

scientific article published on 15 June 2017

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

scientific article published on 01 August 2006

Using AMBER18 for Relative Free Energy Calculations

scientific article published on 20 June 2019

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

scientific article published on April 2016

Validation of AMBER/GAFF for Relative Free Energy Calculations

scientific article published on 4 February 2019

Validation of Free Energy Methods in AMBER

scientific article published on 18 June 2020

Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

scientific article published on 01 January 2005

List of works by Darrin M York

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

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

A charge-scaling implementation of the variational electrostatic projection method

A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields

Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models

Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

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

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations

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

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

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations

Competitive interaction of monovalent cations with DNA from 3D-RISM.

Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis ⬇️

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

Contracted auxiliary Gaussian basis integral and derivative evaluation

DeePMD-kit v2: A software package for deep potential models

Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine

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

Density-functional expansion methods: Grand challenges

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations

Density-functional expansion methods: generalization of the auxiliary basis

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

Design and application of a multicoefficient correlation method for dispersion interactions

Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics

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

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods

Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

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

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

Ellipticity: a convenient tool to characterize electrocyclic reactions

Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

Enzyme transition states from theory and experiment

Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

Exact Relation between Potential of Mean Force and Free-Energy Profile

Exocyclic deoxyadenosine adducts of 1,2,3,4-diepoxybutane: synthesis, structural elucidation, and mechanistic studies

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

Extended polarization in third-order SCC-DFTB from chemical-potential equalization

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

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

Fast approximate methods for calculating nucleic acid base pair interaction energies

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids

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

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

Heavy atom labeled nucleotides for measurement of kinetic isotope effects

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

Hybrid QM/MM study of thio effects in transphosphorylation reactions

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

Identification of dynamical hinge points of the L1 ligase molecular switch

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Improvement of semiempirical response properties with charge-dependent response density

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA.

Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation