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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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A fundamental view of enthalpy-entropy compensation

MedChemComm, 2014, Vol.5 (9), p.1324-1336

Ryde, Ulf

2014

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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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Molecular mechanism of lytic polysaccharide monooxygenases

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

2018

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Reaction mechanism of formate dehydrogenase studied by computational methods

Journal of biological inorganic chemistry, 2018-12, Vol.23 (8), p.1243-1254

2018

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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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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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Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

Journal of biological inorganic chemistry, 2016-06, Vol.21 (3), p.383-394

2016

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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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Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods

Scientific reports, 2023-07, Vol.13 (1), p.10832-10832, Article 10832

2023

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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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Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases

Coordination chemistry reviews, 2013, Vol.257 (2), p.445-458

2013

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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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Histidine oxidation in lytic polysaccharide monooxygenase

Journal of biological inorganic chemistry, 2023-04, Vol.28 (3), p.317-328

2023

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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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Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

Inorganic chemistry, 2018-12, Vol.57 (24), p.15289-15298

2018

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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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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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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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Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?

Dalton transactions : an international journal of inorganic chemistry, 2011-11, Vol.40 (42), p.11176

2011

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

A fundamental view of enthalpy-entropy compensation

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

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

Molecular mechanism of lytic polysaccharide monooxygenases

Reaction mechanism of formate dehydrogenase studied by computational methods

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

On the Difference Between Additive and Subtractive QM/MM Calculations

How to obtain statistically converged MM/GBSA results

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

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

Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods

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

Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases

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

Histidine oxidation in lytic polysaccharide monooxygenase

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

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

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

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

Quantum Crystallography: Current Developments and Future Perspectives

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

Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?

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