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Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

Chemical reviews, 2016-05, Vol.116 (9), p.5520-5566

2016

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Molecular mechanism of lytic polysaccharide monooxygenases

Chemical science (Cambridge), 2018, Vol.9 (15), p.3866-3880

2018

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On the Difference Between Additive and Subtractive QM/MM Calculations

Frontiers in chemistry, 2018-04, Vol.6 (APR), p.89-89

2018

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How to obtain statistically converged MM/GBSA results

Journal of computational chemistry, 2010-03, Vol.31 (4), p.837-846

2010

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The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

Journal of chemical information and modeling, 2012-08, Vol.52 (8), p.2079-2088

2012

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Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding

Journal of the American Chemical Society, 2019-02, Vol.141 (5), p.2012-2026

2019

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QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

Journal of molecular modeling, 2021, Vol.27 (3), p.68-68, Article 68

2021

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Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

Journal of the American Chemical Society, 2010-10, Vol.132 (41), p.14577-14589

2010

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comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

Journal of computational chemistry, 2011-01, Vol.32 (2), p.187-195

2011

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Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

JACS Au, 2021-04, Vol.1 (4), p.484-500

2021

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Quantum Crystallography: Current Developments and Future Perspectives

Chemistry : a European journal, 2018-08, Vol.24 (43), p.10881-10905

2018

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Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

Molecules (Basel, Switzerland), 2023-01, Vol.28 (1), p.65

2023

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Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

Journal of chemical information and modeling, 2011-04, Vol.51 (4), p.947-958

2011

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Quantum Refinement of [FeFe] Hydrogenase Indicates a Dithiomethylamine Ligand

Journal of the American Chemical Society, 2010-04, Vol.132 (13), p.4512-4513

2010

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Unraveling the Binding Mode of Cyclic Adenosine–Inosine Monophosphate to STING through Molecular Dynamics Simulations

Molecules (Basel, Switzerland), 2024-06, Vol.29 (11), p.2650

2024

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Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

Journal of the American Chemical Society, 2011-08, Vol.133 (33), p.13081-13092

2011

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Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

Chemistry : a European journal, 2022-03, Vol.28 (14), p.e202103933-n/a

2022

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fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins

IUCrJ, 2020-03, Vol.7 (Pt 2), p.158-165

2020

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QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I

Results in Chemistry, 2019-01, Vol.1, p.100011, Article 100011

2019

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Multiscale Modelling of Lytic Polysaccharide Monooxygenases

ACS omega, 2017-02, Vol.2 (2), p.536-545

2017

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Reaction Mechanism of Porphyrin Metallation Studied by Theoretical Methods

Chemistry : a European journal, 2005-02, Vol.11 (5), p.1549-1564

2005

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Functionally Relevant Interplay between the Fe4S4 Cluster and CN− Ligands in the Active Site of [FeFe]-Hydrogenases

Journal of the American Chemical Society, 2010-04, Vol.132 (14), p.4992-4993

2010

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Quantum chemical geometry optimizations in proteins using crystallographic raw data

Journal of computational chemistry, 2002-08, Vol.23 (11), p.1058-1070

2002

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Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

Angewandte Chemie (International ed.), 2018-01, Vol.57 (1), p.162-166

International ed. in English, 2018

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A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

Journal of chemical information and modeling, 2014-10, Vol.54 (10), p.2794-2806

2014

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Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

Molecular mechanism of lytic polysaccharide monooxygenases

On the Difference Between Additive and Subtractive QM/MM Calculations

How to obtain statistically converged MM/GBSA results

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

Quantum Crystallography: Current Developments and Future Perspectives

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

Quantum Refinement of [FeFe] Hydrogenase Indicates a Dithiomethylamine Ligand

Unraveling the Binding Mode of Cyclic Adenosine–Inosine Monophosphate to STING through Molecular Dynamics Simulations

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins

QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I

Multiscale Modelling of Lytic Polysaccharide Monooxygenases

Reaction Mechanism of Porphyrin Metallation Studied by Theoretical Methods

Functionally Relevant Interplay between the Fe4S4 Cluster and CN− Ligands in the Active Site of [FeFe]-Hydrogenases

Quantum chemical geometry optimizations in proteins using crystallographic raw data

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

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