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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Expert opinion on drug discovery, 2015-05, Vol.10 (5), p.449-461

2015

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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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Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands

Journal of biological inorganic chemistry, 2021-05, Vol.26 (2-3), p.341-353

2021

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N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods

Journal of biological inorganic chemistry, 2020-05, Vol.25 (3), p.521-540

2020

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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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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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Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

Journal of biological inorganic chemistry, 2020-09, Vol.25 (6), p.847-861

2020

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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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An MM/3D-RISM Approach for Ligand Binding Affinities

The journal of physical chemistry. B, 2010-07, Vol.114 (25), p.8505-8516

2010

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The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

Biochemistry (Easton), 2012-01, Vol.51 (1), p.296-306

2012

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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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Simulation of the isotropic EXAFS spectra for the S₂ and S₃ structures of the oxygen evolving complex in photosystem II

Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (13), p.3979-3984

2015

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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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Large Equatorial Ligand Effects on C–H Bond Activation by Nonheme Iron(IV)-oxo Complexes

The journal of physical chemistry. B, 2014-02, Vol.118 (6), p.1493-1500

2014

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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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Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

Dalton transactions : an international journal of inorganic chemistry, 2024-07, Vol.53 (27), p.115-11513

2024

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Carboxylate Binding Modes in Zinc Proteins: A Theoretical Study

Biophysical journal, 1999-11, Vol.77 (5), p.2777-2787

Ryde, Ulf

1999

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On the role of the axial ligand in heme proteins: a theoretical study

Journal of biological inorganic chemistry, 2004-03, Vol.9 (2), p.203-223

2004

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A QM/MM study of the binding of RAPTA ligands to cathepsin B

Journal of computer-aided molecular design, 2011-08, Vol.25 (8), p.729-742

2011

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QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins

The journal of physical chemistry. B, 2008-10, Vol.112 (39), p.12537-12548

2008

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Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

Proteins, structure, function, and bioinformatics, 2012-05, Vol.80 (5), p.1326-1342

2012

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Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

Inorganics, 2019-11, Vol.7 (11), p.135

2019

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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands

N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods

How to obtain statistically converged MM/GBSA results

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

Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

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

An MM/3D-RISM Approach for Ligand Binding Affinities

The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

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

Quantum Refinement of [FeFe] Hydrogenase Indicates a Dithiomethylamine Ligand

Simulation of the isotropic EXAFS spectra for the S₂ and S₃ structures of the oxygen evolving complex in photosystem II

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

Large Equatorial Ligand Effects on C–H Bond Activation by Nonheme Iron(IV)-oxo Complexes

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

Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

Carboxylate Binding Modes in Zinc Proteins: A Theoretical Study

On the role of the axial ligand in heme proteins: a theoretical study

A QM/MM study of the binding of RAPTA ligands to cathepsin B

QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

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