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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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Extremely large differences in DFT energies for nitrogenase models

Physical chemistry chemical physics : PCCP, 2019, Vol.21 (5), p.2480-2488

2019

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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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Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement

The journal of physical chemistry. B, 2017-09, Vol.121 (35), p.8242-8262

2017

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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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Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

Journal of chemical theory and computation, 2011-08, Vol.7 (8), p.2452-2463

2011

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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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Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

Physical chemistry chemical physics : PCCP, 2012-01, Vol.14 (36), p.12592-1264

2012

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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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Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

Journal of chemical theory and computation, 2013-09, Vol.9 (9), p.4205-4214

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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Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

Journal of chemical theory and computation, 2013-01, Vol.9 (1), p.640-649

2013

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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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How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

Journal of chemical theory and computation, 2017-11, Vol.13 (11), p.5745-5752

Ryde, Ulf

2017

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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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Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

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

2018

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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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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

Extremely large differences in DFT energies for nitrogenase models

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

Molecular mechanism of lytic polysaccharide monooxygenases

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement

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

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

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

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

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

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

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

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

Histidine oxidation in lytic polysaccharide monooxygenase

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

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

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

Quantum Crystallography: Current Developments and Future Perspectives

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