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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 ed.), 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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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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Mechanisms of Anion Conduction by Coupled Glutamate Transporters

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

2015

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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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Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

PLoS computational biology, 2010-01, Vol.6 (1), p.e1000634

2010

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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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Population Shuffling of Protein Conformations

Angewandte Chemie (International ed.), 2015-01, Vol.54 (1), p.207-210

International ed. in English, 2015

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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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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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Crystal structure and functional mechanism of a human antimicrobial membrane channel

Proceedings of the National Academy of Sciences - PNAS, 2013-03, Vol.110 (12), p.4586-4591

2013

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Detection of functional modes in protein dynamics

PLoS computational biology, 2009-08, Vol.5 (8), p.e1000480-e1000480

2009

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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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Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

Biophysical journal, 2012-08, Vol.103 (4), p.786-796

2012

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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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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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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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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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Probing the energy landscape of activation gating of the bacterial potassium channel KcsA

PLoS computational biology, 2013-05, Vol.9 (5), p.e1003058

2013

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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

A molecular mechanism for transthyretin amyloidogenesis

Crystal Structure of an Ammonia-Permeable Aquaporin

Mechanisms of Anion Conduction by Coupled Glutamate Transporters

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

Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

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

Population Shuffling of Protein Conformations

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

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

Crystal structure and functional mechanism of a human antimicrobial membrane channel

Detection of functional modes in protein dynamics

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

Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

The Persistent Question of Potassium Channel Permeation Mechanisms

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

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

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

Probing the energy landscape of activation gating of the bacterial potassium channel KcsA

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