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More bang for your buck: Improved use of GPU nodes for GROMACS 2018

Journal of computational chemistry, 2019-10, Vol.40 (27), p.2418-2431

2019

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Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Journal of computer-aided molecular design, 2010-05, Vol.24 (5), p.417-422

2010

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Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail

Biophysical journal, 2011-08, Vol.101 (4), p.809-817

2011

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Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

Angewandte Chemie International Edition, 2016-06, Vol.55 (26), p.7364-7368

International ed. in English, 2016

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Lipid-protein interactions modulate the conformational equilibrium of a potassium channel

Nature communications, 2020-05, Vol.11 (1), p.2162-2162, Article 2162

2020

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Central cavity dehydration as a gating mechanism of potassium channels

Nature communications, 2023-04, Vol.14 (1), p.2178-12, Article 2178

2023

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Mechanism of selectivity in aquaporins and aquaglyceroporins

Proceedings of the National Academy of Sciences - PNAS, 2008-01, Vol.105 (4), p.1198-1203

2008

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Nature methods, 2017-01, Vol.14 (1), p.71-73

2017

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A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K+ Channels

Cell, 2016-02, Vol.164 (5), p.937-949

2016

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Resolving coupled pH titrations using alchemical free energy calculations

Journal of computational chemistry, 2024-06, Vol.45 (17), p.1444-1455

2024

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A molecular mechanism for transthyretin amyloidogenesis

Nature communications, 2019-02, Vol.10 (1), p.925-925, Article 925

2019

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Crystal Structure of an Ammonia-Permeable Aquaporin

PLoS biology, 2016-03, Vol.14 (3), p.e1002411-e1002411

2016

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Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling

Nature communications, 2019-11, Vol.10 (1), p.5366-15, Article 5366

2019

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Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

Methods in molecular biology (Clifton, N.J.), 2019-01, Vol.1851, p.19

2019

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The Persistent Question of Potassium Channel Permeation Mechanisms

Journal of molecular biology, 2021-08, Vol.433 (17), p.167002-167002, Article 167002

2021

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Mechanisms of Anion Conduction by Coupled Glutamate Transporters

Cell, 2015-01, Vol.160 (3), p.542-553

2015

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pmx: Automated protein structure and topology generation for alchemical perturbations

Journal of computational chemistry, 2015-02, Vol.36 (5), p.348-354

2015

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On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

eLife, 2020-08, Vol.9

2020

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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Journal of computer-aided molecular design, 2020-05, Vol.34 (5), p.601-633

2020

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Identification of kinetic order parameters for non-equilibrium dynamics

The Journal of chemical physics, 2019-04, Vol.150 (16), p.164120

2019

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Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

eLife, 2019-06, Vol.8

2019

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Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Chemical science (Cambridge), 2020, Vol.11 (4), p.1140-1152

2020

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g_whamA Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Journal of chemical theory and computation, 2010-12, Vol.6 (12), p.3713-3720

2010

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Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

Journal of chemical theory and computation, 2015-11, Vol.11 (11), p.5513-5524

2015

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Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

Communications chemistry, 2021-05, Vol.4 (1), p.61-61, Article 61

2021

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More bang for your buck: Improved use of GPU nodes for GROMACS 2018

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

Lipid-protein interactions modulate the conformational equilibrium of a potassium channel

Central cavity dehydration as a gating mechanism of potassium channels

Mechanism of selectivity in aquaporins and aquaglyceroporins

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K+ Channels

Resolving coupled pH titrations using alchemical free energy calculations

A molecular mechanism for transthyretin amyloidogenesis

Crystal Structure of an Ammonia-Permeable Aquaporin

Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

The Persistent Question of Potassium Channel Permeation Mechanisms

Mechanisms of Anion Conduction by Coupled Glutamate Transporters

pmx: Automated protein structure and topology generation for alchemical perturbations

On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Identification of kinetic order parameters for non-equilibrium dynamics

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

g_whamA Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

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