List of works - Samuel Genheden

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

scientific article published on 24 June 2011

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

scientific article published on January 30, 2011

A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.

scientific article

A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections

scientific article published on 07 March 2012

A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes

scientific article published on 08 September 2015

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

scientific article published on 29 July 2011

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

scientific article published on 26 July 2016

Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis.

scientific article

An MM/3D-RISM approach for ligand binding affinities.

scientific article published in July 2010

Are Homology Models Sufficiently Good for Free-Energy Simulations? ⬇️

scientific article published on November 12, 2012

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

scientific article published on 17 August 2015

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

article

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

scientific article published on 18 March 2011

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

scientific article

Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models.

scientific article published on 15 November 2015

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

scientific article published on 13 February 2012

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

scientific article published on 19 October 2011

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

scientific article published on 01 January 2014

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

scientific article

Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

scientific article

Effect of solvent model when probing protein dynamics with molecular dynamics.

scientific article

Estimates of ligand-binding affinities supported by quantum mechanical methods.

scientific article published on 28 January 2010

Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models

scientific article published on 31 August 2016

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

scientific article published in February 2014

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

scientific article published on 04 April 2014

G protein coupled receptor interactions with cholesterol deep in the membrane

scientific article published on 2 December 2016

How to obtain statistically converged MM/GBSA results.

scientific article published in March 2010

Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation

scientific article published on 12 March 2012

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model ⬇️

scientific article published on November 19, 2011

Mechanism of Trehalose-Induced Protein Stabilization from Neutron Scattering and Modeling

scientific article published on 18 April 2019

Nonpolar Solvation Free Energies of Protein-Ligand Complexes

scientific article published on 28 September 2010

Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin.

scientific article published on 15 December 2013

PaRoutes: towards a framework for benchmarking retrosynthesis route predictions

scientific article published in January 2022

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

scientific article published on 11 December 2015

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

scientific article

Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii.

scientific article published on 29 September 2015

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.

scientific article published on July 2010

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

scientific article

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

scientific article

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

scientific article published on 02 August 2012

Will molecular dynamics simulations of proteins ever reach equilibrium? ⬇️

scientific article published on May 22, 2012

List of works by Samuel Genheden

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

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

A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.

A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections

A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis.

An MM/3D-RISM approach for ligand binding affinities.

Are Homology Models Sufficiently Good for Free-Energy Simulations? ⬇️

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models.

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

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

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

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

Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

Effect of solvent model when probing protein dynamics with molecular dynamics.

Estimates of ligand-binding affinities supported by quantum mechanical methods.

Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

G protein coupled receptor interactions with cholesterol deep in the membrane

How to obtain statistically converged MM/GBSA results.

Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation

MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model ⬇️

Mechanism of Trehalose-Induced Protein Stabilization from Neutron Scattering and Modeling

Nonpolar Solvation Free Energies of Protein-Ligand Complexes

Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin.

PaRoutes: towards a framework for benchmarking retrosynthesis route predictions

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

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

Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii.

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.

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

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

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

Will molecular dynamics simulations of proteins ever reach equilibrium? ⬇️