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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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AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

Journal of cheminformatics, 2020-11, Vol.12 (1), p.70-70, Article 70

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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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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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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Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii

Biotechnology and bioengineering, 2016-04, Vol.113 (4), p.744-753

2016

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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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Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae

Scientific reports, 2021-08, Vol.11 (1), p.17333-17333, Article 17333

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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AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application

Journal of cheminformatics, 2024-05, Vol.16 (1), p.57-57, Article 57

2024

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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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Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model

Journal of chemical theory and computation, 2016-01, Vol.12 (1), p.297-304

Genheden, Samuel

2016

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AI for drug design: From explicit rules to deep learning

Artificial intelligence in the life sciences, 2022-12, Vol.2, p.100041, Article 100041

2022

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Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

Journal of computer-aided molecular design, 2017-10, Vol.31 (10), p.867-876

Genheden, Samuel

2017

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Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition

Journal of cheminformatics, 2024-04, Vol.16 (1), p.39-39, Article 39

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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Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3

Journal of biomolecular NMR, 2009-09, Vol.45 (1-2), p.157-169

2009

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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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A Hybrid All-Atom/Coarse-Grained Approach to Problems in Chemistry and Biology

Biophysical journal, 2017-02, Vol.112 (3), p.177a-177a

Genheden, Samuel

2017

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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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Will molecular dynamics simulations of proteins ever reach equilibrium?

Physical chemistry chemical physics : PCCP, 2012-01, Vol.14 (24), p.8662-8677

2012

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Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

Journal of chemical theory and computation, 2011-11, Vol.7 (11), p.3768-3778

2011

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PaRoutes: towards a framework for benchmarking retrosynthesis route predictions

Digital discovery, 2022-08, Vol.1 (4), p.527-539

2022

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Effect of solvent model when probing protein dynamics with molecular dynamics

Journal of molecular graphics & modelling, 2017-01, Vol.71, p.80-87

Genheden, Samuel

2017

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

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

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

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

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

Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii

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

Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae

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

AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application

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

Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model

AI for drug design: From explicit rules to deep learning

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition

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

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3

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

A Hybrid All-Atom/Coarse-Grained Approach to Problems in Chemistry and Biology

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

Will molecular dynamics simulations of proteins ever reach equilibrium?

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

PaRoutes: towards a framework for benchmarking retrosynthesis route predictions

Effect of solvent model when probing protein dynamics with molecular dynamics

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