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Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

RNA (Cambridge), 2015-09, Vol.21 (9), p.1578-1590

2015

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Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry

Biochimica et biophysica acta, 2017-02, Vol.1861 (2), p.485-498

2017

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HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host–Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions

The journal of physical chemistry. B, 2017-12, Vol.121 (49), p.11144-11162

2017

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Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters

Journal of chemical theory and computation, 2017-09, Vol.13 (9), p.4253-4269

2017

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Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

Journal of chemical theory and computation, 2017-07, Vol.13 (7), p.3260-3275

2017

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Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

Journal of chemical theory and computation, 2015-09, Vol.11 (9), p.4377-4394

2015

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Araiosamines A−D: Tris-bromoindole Cyclic Guanidine Alkaloids from the Marine Sponge Clathria (Thalysias) araiosa

Journal of organic chemistry, 2011-07, Vol.76 (14), p.5515-5523

2011

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Overview of the SAMPL5 host–guest challenge: Are we doing better?

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.1-19

2017

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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Journal of computer-aided molecular design, 2020-05, Vol.34 (5), p.601-633

2020

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Bind3P: Optimization of a Water Model Based on Host–Guest Binding Data

Journal of chemical theory and computation, 2018-07, Vol.14 (7), p.3621-3632

2018

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Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

Journal of chemical theory and computation, 2014-09, Vol.10 (9), p.4069-4078

2014

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Accounting for apparent deviations between calorimetric and van't Hoff enthalpies

Biochimica et biophysica acta. General subjects, 2018-03, Vol.1862 (3), p.692-704

2018

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Journal of chemical theory and computation, 2014-01, Vol.10 (1), p.492-499

2014

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Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin

Journal of the American Chemical Society, 2019-07, Vol.141 (30), p.11765-11769

2019

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Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations

Journal of chemical theory and computation, 2018-03, Vol.14 (3), p.1456-1470

2018

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Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

The journal of physical chemistry. B, 2015-08, Vol.119 (32), p.10145-10155

2015

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Binding Thermodynamics of Host–Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Journal of chemical theory and computation, 2019-11, Vol.15 (11), p.6225-6242

2019

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The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.133-145

2017

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Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters

Journal of chemical theory and computation, 2020-02, Vol.16 (2), p.1115-1127

2020

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Synthesis and Evaluation of 1,3-Disubstituted Imidazolidine-2,4,5-triones as Inhibitors of Pyruvate Carboxylase

ACS medicinal chemistry letters, 2024-07, Vol.15 (7), p.1088-1093

2024

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Binding Enthalpy Calculations for a Neutral Host–Guest Pair Yield Widely Divergent Salt Effects across Water Models

Journal of chemical theory and computation, 2015-10, Vol.11 (10), p.4555-4564

2015

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Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

The journal of physical chemistry. B, 2013-04, Vol.117 (15), p.4014-4027

2013

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AI Based Discovery of a New AKR1C3 Inhibitor for Anticancer Applications

ACS medicinal chemistry letters, 2024-08, Vol.15 (8), p.1269-1278

2024

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Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase

Archives of biochemistry and biophysics, 2017-01, Vol.613, p.1-11

2017

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Structural and Energetic Analysis of 2‑Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

Journal of chemical information and modeling, 2014-06, Vol.54 (6), p.1758-1772

2014

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Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry

HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host–Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

Araiosamines A−D: Tris-bromoindole Cyclic Guanidine Alkaloids from the Marine Sponge Clathria (Thalysias) araiosa

Overview of the SAMPL5 host–guest challenge: Are we doing better?

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Bind3P: Optimization of a Water Model Based on Host–Guest Binding Data

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin

Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

Binding Thermodynamics of Host–Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters

Synthesis and Evaluation of 1,3-Disubstituted Imidazolidine-2,4,5-triones as Inhibitors of Pyruvate Carboxylase

Binding Enthalpy Calculations for a Neutral Host–Guest Pair Yield Widely Divergent Salt Effects across Water Models

Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

AI Based Discovery of a New AKR1C3 Inhibitor for Anticancer Applications

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase

Structural and Energetic Analysis of 2‑Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

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