Jérôme Hénin Jérôme Hénin - Curriculum vitae

Publications

Article dans une revue (41)

Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors Narjes Ansari,Chengwen Liu,Florent Hedin,Jérôme Hénin,Jay W. Ponderet al. Communications Biology, 2025, 8, pp.1405. ⟨10.1038/s42003-025-08809-y⟩ Article dans une revue hal-04742743v3
Allosteric coupling between a lipid bilayer and a membrane protein Clarisse Fourel,Yanna Gautier,Alexandre Pozza,François Giraud,Elodie Pointet al. Biophysical Journal, 2025, ⟨10.1016/j.bpj.2025.06.033⟩ Article dans une revue hal-04954807v1
Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors Narjes Ansari,Chengwen Liu,Florent Hédin,Jérôme Hénin,Jay W Ponderet al. Communications Biology, 2025, 8 (1), pp.1405. ⟨10.1038/s42003-025-08809-y⟩ Article dans une revue hal-05498925v1
Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations Narjes Ansari,Zhifeng Francis Jing,Antoine Gagelin,Florent Hédin,Félix Aviatet al. Journal of Physical Chemistry Letters, 2025, 16 (19), pp.4626-4634. ⟨10.1021/acs.jpclett.5c00683⟩ Article dans une revue hal-05481035v1
k-Nearest Neighbor Adaptive Sampling, a Simple Tool to Efficiently Explore Conformational Space Evianne Rovers,Anvith Thudi,Jérôme Hénin,Chris Maddison,Matthieu Schapira Journal of Chemical Theory and Computation, 2025, 21 (17), pp.8267-8277. ⟨10.1021/acs.jctc.5c00462⟩ Article dans une revue hal-05241482v1
Calculating free-energy differences using an average force: A tutorial for adaptive biasing force simulations Radu Talmazan,Haohao Fu,Mengchen Zhou,Jérôme Hénin,James Gumbartet al. Journal of Physical Chemistry B, 2025, 129 (39), pp.9913-9928. ⟨10.1021/acs.jpcb.5c04333⟩ Article dans une revue hal-05412282v1
Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations Narjes Ansari,Zhifeng Francis Jing,Antoine Gagelin,Florent Hédin,Félix Aviatet al. Journal of Physical Chemistry Letters, 2025, 16, pp.4626-4634. ⟨10.1021/acs.jpclett.5c00683⟩ Article dans une revue hal-04964833v1
Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations Louis Lagardère,Lise Maurin,Olivier Adjoua,Krystel El Hage,Pierre Monmarchéet al. Journal of Chemical Theory and Computation, 2024, ⟨10.48550/arXiv.2307.08006⟩ Article dans une revue hal-04162777v1
alchemlyb: the simple alchemistry library Zhiyi Wu,David Dotson,Irfan Alibay,Bryce Allen,Mohammad Soroush Barhaghiet al. Journal of Open Source Software, 2024, 9 (101), pp.6934. ⟨10.21105/joss.06934⟩ Article dans une revue hal-04752550v1
Expanded functionality and portability for the Colvars library Giacomo Fiorin,Fabrizio Marinelli,Lucy Forrest,Haochuan Chen,Christophe Chipotet al. Journal of Physical Chemistry B, 2024, 128 (45), pp.11108-11123. ⟨10.1021/acs.jpcb.4c05604⟩ Article dans une revue hal-04782969v1
Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling Antoine Gagelin,Corentin Largeau,Sandrine Masscheleyn,Mathilde Piel,Daniel Calderón-Moraet al. Nature Communications, 2023, 14 (1), pp.2594. ⟨10.1101/2022.12.09.516457⟩ Article dans une revue hal-04018865v1
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
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-04728951v1
Alchemical Free Energy Calculations on Membrane-Associated Proteins Michail Papadourakis,Hryhory Sinenka,Pierre Matricon,Jérôme Hénin,Grace Branniganet al. Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.3c00365⟩ Article dans une revue hal-04265307v1
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 Washingtonet al. 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
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
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
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
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
Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations Xiaojing Wu,Jérôme Hénin,Laura Baciou,Marc Baaden,Fabien Cailliezet al. Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩ Article dans une revue hal-03382660v1
Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry Elise Duboué-Dijon,Jérôme Hénin The 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
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-Searaet al. 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 Ribeiroet al. The 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
A membrane-inserted structural model of the yeast mitofusin Fzo1 Dario de Vecchis,Laetitia Cavellini,Marc Baaden,Jérôme Hénin,Mickaël M. Cohenet al. Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩ Article dans une revue hal-01581980v1
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 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 Wanget al. Journal of Biological Chemistry, 2016, 291, pp.20473--86. ⟨10.1074/jbc.M116.736975⟩ Article dans une revue hal-01497996v1
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
Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. Zoe Cournia,Toby Allen,Ioan Andricioaei,Bruno Antonny,Daniel Baumet al. Journal of Membrane Biology, 2015, 248 (4), pp.611-640. ⟨10.1007/s00232-015-9802-0⟩ Article dans une revue (article de synthèse) hal-01498031v1
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
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 Pohorilleet al. Journal of Physical Chemistry B, 2015, 119 (3), pp.1129-1151. ⟨10.1021/jp506633n⟩ Article dans une revue hal-01238593v1
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.315-321. ⟨10.1002/embr.201337936⟩ Article dans une revue hal-01458198v1
CHARMM36 united atom chain model for lipids and surfactants. Sarah Lee,Alan Tran,Matthew Allsopp,Joseph B. Lim,Jérôme Héninet al. Journal of Physical Chemistry B, 2014, 118 (2), pp.547--556. ⟨10.1021/jp410344g⟩ Article dans une revue hal-01498054v1
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
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. Williamsonet al. Langmuir, 2014, 30 (21), pp.6162-6170. ⟨10.1021/la5004353⟩ Article dans une revue hal-01498056v1
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
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

Communication dans un congrès (2)

UnityMol-Lite: Cross-platform Collaboration and Interactive Methods for Molecular Modeling in XR Mariano Spivak,Bastien Vincke,Hubert Santuz,Jérôme Hénin,Antoine Talyet al. EuroXR 2024: Proceedings of the 21st EuroXR International Conference, Patrick Bourdot; Mónica González; Jerome Perret; Gabriel Zachmann; Arcadio Reyes-Lecuona, Nov 2024, Athens, Greece Communication dans un congrès hal-05163459v1
Simulation moléculaire du transfert d’électron transmembranaire dans NOX5 F. Cailliez,Xiaojing Wu,Jérôme Hénin,Laura Baciou,Marc Baadenet al. 3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France Communication dans un congrès hal-04426169v1

Chapitre d'ouvrage (2)

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

Pré-publication, Document de travail (2)

Fast, systematic and robust relative binding free energies for simple and complex transformations : dual-LAO Narjes Ansari,Félix Aviat,Jérôme Hénin,Jean-Philip Piquemal,Louis Lagardère 2025 Pré-publication, Document de travail hal-05428437v1
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

Thèse (1)

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