Jérôme Hénin

Jérôme Hénin - Curriculum vitae

Documents

Publications

	Computing absolute binding affinities by Streamlined Alchemical Free Energy Perturbation [Article v1.0] Ezry Santiago-Mcrae , Mina Ebrahimi , Jesse Sandberg , Grace Brannigan , Jérôme Hénin Living Journal of Computational Molecular Science, 2023, 5 (1), ⟨10.33011/livecoms.5.1.2067⟩ Article dans une revue hal-04265411v1
	Alchemical Free Energy Calculations on Membrane-Associated Proteins Michail Papadourakis , Hryhory Sinenka , Pierre Matricon , Jérôme Hénin , Grace Brannigan Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.3c00365⟩ Article dans une revue hal-04265307v1
	Unwrapping NPT Simulations to Calculate Diffusion Coefficients Jakob Tómas Bullerjahn , Sören von Bülow , Maziar Heidari , Jérôme Hénin , Gerhard Hummer Journal of Chemical Theory and Computation, 2023, 19 (11), pp.3406-3417. ⟨10.1021/acs.jctc.3c00308⟩ Article dans une revue hal-04228524v1
	Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2 Cecilia Chávez-García , Jérôme Hénin , Mikko Karttunen Journal of Chemical Information and Modeling, 2022, 62 (4), pp.958-970. ⟨10.1021/acs.jcim.1c01354⟩ Article dans une revue hal-03689392v1
	Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation John Petroff , Noah Dietzen , Ezry Santiago-Mcrae , Brett Deng , Maya Washington Nature Communications, 2022, 13 (1), pp.7017. ⟨10.1038/s41467-022-34813-5⟩ Article dans une revue hal-03858898v1
	Enhanced sampling methods for molecular dynamics simulations Jérôme Hénin , Tony Lelièvre , Michael Shirts , Omar Valsson , Lucie Delemotte Living Journal of Computational Molecular Science, 2022, 4 (1), ⟨10.33011/livecoms.4.1.1583⟩ Article dans une revue hal-03595710v1
	Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling Antoine Gagelin , Corentin Largeau , Sandrine Masscheleyn , Mathilde Piel , Daniel Calderón-Mora Nature Communications, 2022, 14 (1), pp.2594. ⟨10.1101/2022.12.09.516457⟩ Article dans une revue hal-04018865v1
	Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD Jérôme Hénin , Laura Lopes , Giacomo Fiorin Journal of Chemical Theory and Computation, 2022, 18 (3), pp.1945-1956. ⟨10.1021/acs.jctc.1c01081⟩ Article dans une revue hal-03689385v1
	A consistent picture of phosphate-divalent cation binding from models with implicit and explicit electronic polarization Julie Puyo-Fourtine , Marie Juillé , Jérôme Hénin , Carine Clavaguéra , Elise Duboué-Dijon Journal of Physical Chemistry B, 2022, 126 (22), pp.4022-4034. ⟨10.1021/acs.jpcb.2c01158⟩ Article dans une revue hal-03677547v1
	Symmetry-Adapted Restraints for Binding Free Energy Calculations Mina Ebrahimi , Jérôme Hénin Journal of Chemical Theory and Computation, 2022, 18 (4), pp.2494-2502. ⟨10.1021/acs.jctc.1c01235⟩ Article dans une revue hal-03667626v1
	Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry Elise Duboué-Dijon , Jérôme Hénin Journal of Chemical Physics, 2021, 154 (20), pp.204101. ⟨10.1063/5.0046853⟩ Article dans une revue hal-03234443v1
	Fast and Accurate Multidimensional Free Energy Integration Jérôme Hénin Journal of Chemical Theory and Computation, 2021, 17 (11), pp.6789-6798. ⟨10.1021/acs.jctc.1c00593⟩ Article dans une revue hal-03402188v1
	Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations Xiaojing Wu , Jérôme Hénin , Laura Baciou , Marc Baaden , Fabien Cailliez Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩ Article dans une revue hal-03382660v1
	Binding of Divalent Cations to Aqueous Acetate: Molecular Simulations Guided by Raman Spectroscopy Denilson Mendes de Oliveira , Samual R Zukowski , Vladimir Palivec , Jérôme Hénin , Hector Martinez-Seara Physical Chemistry Chemical Physics, 2020, ⟨10.1039/D0CP02987D⟩ Article dans une revue hal-02964203v1
	Scalable molecular dynamics on CPU and GPU architectures with NAMD James Phillips , David J. Hardy , Julio Maia , John Stone , João Ribeiro Journal of Chemical Physics, 2020, 153 (4), pp.044130. ⟨10.1063/5.0014475⟩ Article dans une revue hal-03032818v1
	A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol Reza Salari , Thomas Joseph , Ruchi Lohia , Jérôme Hénin , Grace Brannigan Journal of Chemical Theory and Computation, 2018, 14 (12), pp.6560-6573. ⟨10.1021/acs.jctc.8b00447⟩ Article dans une revue hal-02540263v1
	Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method Adrien Lesage , Tony Lelièvre , Gabriel Stoltz , Jérôme Hénin Journal of Physical Chemistry B, 2017, 121 (15), pp.3676-3685. ⟨10.1021/acs.jpcb.6b10055⟩ Article dans une revue hal-01423958v1
	New Coarse Variables for the Accurate Determination of Standard Binding Free Energies Haohao Fu , Wensheng Cai , Jérôme Hénin , Benoît Roux , Christophe Chipot Journal of Chemical Theory and Computation, 2017, 13 (11), pp.5173-5178. ⟨10.1021/acs.jctc.7b00791⟩ Article dans une revue hal-04054596v1
	A membrane-inserted structural model of the yeast mitofusin Fzo1 Dario de Vecchis , Laetitia Cavellini , Marc Baaden , Jérôme Hénin , Mickaël M. Cohen Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩ Article dans une revue hal-01581980v1
	Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. Mariama Jaiteh , Antoine Taly , Jérôme Hénin PLoS ONE, 2016, 11, pp.e0151934. ⟨10.1371/journal.pone.0151934⟩ Article dans une revue hal-01497980v1
	A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of gamma-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes. Kellie A. Woll , Sruthi Murlidaran , Benika J. Pinch , Jérôme Hénin , Xiaoshi Wang Journal of Biological Chemistry, 2016, 291, pp.20473--86. ⟨10.1074/jbc.M116.736975⟩ Article dans une revue hal-01497996v1
	Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. Zoe Cournia , Toby Allen , Ioan Andricioaei , Bruno Antonny , Daniel Baum Journal of Membrane Biology, 2015, 248 (4), pp.611-640. ⟨10.1007/s00232-015-9802-0⟩ Article dans une revue hal-01498031v1
	The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask Jeffrey Comer , James C. Gumbart , Jérôme Hénin , Tony Lelièvre , Andrew Pohorille Journal of Physical Chemistry B, 2015, 119 (3), pp.1129-1151. ⟨10.1021/jp506633n⟩ Article dans une revue hal-01238593v1
	Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. Obaidur Rahaman , Maria Kalimeri , Simone Melchionna , Jérôme Hénin , Fabio Sterpone Journal of Physical Chemistry B, 2015, 119, pp.8939--49. ⟨10.1021/jp507571u⟩ Article dans une revue hal-01498026v1
	Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective Antoine Taly , Jérôme Hénin , Jean-Pierre Changeux , Marco Cecchini Channels, 2014, 8 (4), pp.350-360. ⟨10.4161/chan.29444⟩ Article dans une revue hal-01498037v1
	A predicted binding site for cholesterol on the GABAA receptor. Jérôme Hénin , Reza Salari , Sruthi Murlidaran , Grace Brannigan Biophysical Journal, 2014, 106 (9), pp.1938--1949. ⟨10.1016/j.bpj.2014.03.024⟩ Article dans une revue hal-01498058v1
	Lipid concentration and molar ratio boundaries for the use of isotropic bicelles. Maïwenn Beaugrand , Alexandre A. Arnold , Jérôme Hénin , Dror E. Warschawski , Philip T F. Williamson Langmuir, 2014, 30 (21), pp.6162-6170. ⟨10.1021/la5004353⟩ Article dans une revue hal-01498056v1
	Type VI secretion and bacteriophage tail tubes share a common assembly pathway Yannick Brunet , Jérôme Hénin , Hervé Celia , E. Cascales EMBO Reports, 2014, 15 (3), pp.315-321. ⟨10.1002/embr.201337936⟩ Article dans une revue hal-03274782v1
	CHARMM36 united atom chain model for lipids and surfactants. Sarah Lee , Alan Tran , Matthew Allsopp , Joseph B. Lim , Jérôme Hénin Journal of Physical Chemistry B, 2014, 118 (2), pp.547--556. ⟨10.1021/jp410344g⟩ Article dans une revue hal-01498054v1
	Type VI secretion and bacteriophage tail tubes share a common assembly pathway. Yannick R Brunet , Jérôme Hénin , Hervé H. Celia , E. Cascales EMBO Reports, 2014, 15 (3), pp.315--21. ⟨10.1002/embr.201337936⟩ Article dans une revue hal-01458198v1
	Using collective variables to drive molecular dynamics simulations Giacomo Fiorin , Michael L. Klein , Jérôme Hénin Mol. Phys., 2013, 111 (22-23), pp.3345--3362. ⟨10.1080/00268976.2013.813594⟩ Article dans une revue hal-01498073v1
	General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity David N. Lebard , Jérôme Hénin , Roderic G. Eckenhoff , Michael L. Klein , Grace Brannigan PLoS Computational Biology, 2012, 8 (5), pp.e1002532. ⟨10.1371/journal.pcbi.1002532⟩ Article dans une revue hal-01498104v1

	Simulation moléculaire du transfert d’électron transmembranaire dans NOX5 F. Cailliez , Xiaojing Wu , Jérôme Hénin , Laura Baciou , Marc Baaden 3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France Communication dans un congrès hal-04426169v1

	Molecular Mechanics Parameterization of Anesthetic Molecules Thomas Joseph , Jérôme Hénin Chemical and Biochemical Approaches for the Study of Anesthetic Function, Part A, 602, Elsevier, pp.61-76, 2018, Methods in Enzymology, ⟨10.1016/bs.mie.2018.01.003⟩ Chapitre d'ouvrage hal-03692578v1
	Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins Jérôme Hénin , Marc Baaden , Antoine Taly Membrane Proteins Production for Structural Analysis, Springer New York, pp.347--392, 2014, 978-1-4939-0661-1. ⟨10.1007/978-1-4939-0662-8_13⟩ Chapitre d'ouvrage hal-01498051v1

	Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations Louis Lagardère , Lise Maurin , Olivier Adjoua , Krystel EL Hage , Pierre Monmarché 2023 Pré-publication, Document de travail hal-04162777v1
	Designing losses for data-free training of normalizing flows on Boltzmann distributions Loris Felardos , Jérôme Hénin , Guillaume Charpiat 2023 Pré-publication, Document de travail hal-03936982v1

	Simulations moléculaires d'événements rares dans les systèmes biologiques membranaires Jérôme Hénin Biologie moléculaire. Université Henri Poincaré - Nancy 1, 2006. Français. ⟨NNT : 2006NAN10007⟩ Thèse tel-01746639v1

Jérôme Hénin

Publications

Computing absolute binding affinities by Streamlined Alchemical Free Energy Perturbation [Article v1.0]

Alchemical Free Energy Calculations on Membrane-Associated Proteins

Unwrapping NPT Simulations to Calculate Diffusion Coefficients

Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2

Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation

Enhanced sampling methods for molecular dynamics simulations

Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling

Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD

A consistent picture of phosphate-divalent cation binding from models with implicit and explicit electronic polarization

Symmetry-Adapted Restraints for Binding Free Energy Calculations

Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry

Fast and Accurate Multidimensional Free Energy Integration

Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations

Binding of Divalent Cations to Aqueous Acetate: Molecular Simulations Guided by Raman Spectroscopy

Scalable molecular dynamics on CPU and GPU architectures with NAMD

A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

A membrane-inserted structural model of the yeast mitofusin Fzo1

Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.

A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of gamma-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes.

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.

Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective

A predicted binding site for cholesterol on the GABAA receptor.

Lipid concentration and molar ratio boundaries for the use of isotropic bicelles.

Type VI secretion and bacteriophage tail tubes share a common assembly pathway

CHARMM36 united atom chain model for lipids and surfactants.

Type VI secretion and bacteriophage tail tubes share a common assembly pathway.

Using collective variables to drive molecular dynamics simulations

General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity

Simulation moléculaire du transfert d’électron transmembranaire dans NOX5

Molecular Mechanics Parameterization of Anesthetic Molecules

Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins

Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations

Designing losses for data-free training of normalizing flows on Boltzmann distributions

Simulations moléculaires d'événements rares dans les systèmes biologiques membranaires