Samuel Murail

Maître de Conférence (Université Paris Cité)
36
Documents

Publications

Publications

Deposit thumbnail

Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events

Dirk Stratmann , Gautier Moroy , Pierre Tuffery , Samuel Murail

Journal of Chemical Theory and Computation, 2025, 21 (21), pp.10705-10718. ⟨10.1021/acs.jctc.5c00950⟩

Article dans une revue hal-05415864v1
Deposit thumbnail

Af-analysis: a Python package for Alphafold analysis

Alaa Reguei , Samuel Murail

Journal of Open Source Software, 2025, 10 (107), pp.7577. ⟨10.21105/joss.07577⟩

Article dans une revue hal-05415824v1
Deposit thumbnail

State-dependent dynamic communication networks in a pentameric ligand-gated ion channel

Bogdan Lev , Samuel Murail , Igor Vorobyov , Marc Baaden , Toby Allen

Journal of Physical Chemistry B, 2025, 129 (37), pp.9333-9356. ⟨10.1021/acs.jpcb.5c03991⟩

Article dans une revue hal-05412186v1
Deposit thumbnail

Exploring the interaction between a LRRK2/PP1CA interfering peptide and PP1CA

Jose Dominguez-Meijide , Samuel Murail , Rachid Boudjelloul , Pierre Tuffery , Angelita Rebollo

Journal of Molecular Graphics and Modelling, 2025, 141, pp.109140. ⟨10.1016/j.jmgm.2025.109140⟩

Article dans une revue hal-05349371v1
Deposit thumbnail

Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields

Samuel Murail , Jaysen Sawmynaden , Akli Zemirli , Maud Jusot , Fabio Pietrucci et al.

Journal of Chemical Theory and Computation, 2025, 21 (19), pp.10018-10034. ⟨10.1021/acs.jctc.5c01123⟩

Article dans une revue hal-05415840v1
Deposit thumbnail

Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships

Guillaume Ollitrault , Rayane Achebouche , Antoine Dreux , Samuel Murail , Karine Audouze et al.

Nucleic Acids Research, 2024, 52 (W1), pp.W507-W512. ⟨10.1093/nar/gkae305⟩

Article dans une revue hal-04665721v1
Deposit thumbnail

In Silico and In Vivo Studies of a Tumor-Penetrating and Interfering Peptide with Antitumoral Effect on Xenograft Models of Breast Cancer

Gustavo H Marin , Samuel Murail , Laura Andrini , Marcela Garcia , Severine Loisel et al.

Pharmaceutics, 2023, 15 (4), pp.1180. ⟨10.3390/pharmaceutics15041180⟩

Article dans une revue hal-05441860v1
Deposit thumbnail

Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization

Yasaman Karami , Samuel Murail , Julien Giribaldi , Benjamin Lefranc , Florian Defontaine et al.

Journal of Chemical Information and Modeling, 2023, 63 (20), pp.6436-6450. ⟨10.1021/acs.jcim.3c00865⟩

Article dans une revue (article de synthèse) hal-04406845v1
Deposit thumbnail

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution

Julien Rey , Samuel Murail , Sjoerd de Vries , Philippe Derreumaux , Pierre Tuffery

Nucleic Acids Research, 2023, 51 (W1), pp.W432-W437. ⟨10.1093/nar/gkad376⟩

Article dans une revue hal-05441879v1
Deposit thumbnail

Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h

Karim Dorgham , Samuel Murail , Pierre Tuffery , Eric Savier , Jeronimo Bravo et al.

Pharmaceutics, 2022, 14 (10), pp.2055. ⟨10.3390/pharmaceutics14102055⟩

Article dans une revue hal-03794499v1
Deposit thumbnail

InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps

Chloe Quignot , Guillaume Postic , Helene Bret , Julien Rey , Pierre Granger et al.

Nucleic Acids Research, 2021, 49 (W1), pp.W277-W284. ⟨10.1093/nar/gkab358⟩

Article dans une revue hal-03677216v1
Deposit thumbnail

Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs

Arthur Hardiagon , Samuel Murail , Li-Bo Huang , Arie van Der Lee , Fabio Sterpone et al.

The Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩

Article dans une revue hal-03410227v1
Deposit thumbnail

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking

Samuel Murail , Sjoerd J. de Vries , Julien Rey , Gautier Moroy , Pierre Tuffery

Frontiers in Molecular Biosciences, 2021, 8, ⟨10.3389/fmolb.2021.716466⟩

Article dans une revue hal-03677201v1
Deposit thumbnail

Glutathionylation primes soluble GAPDH for late collapse into insoluble aggregates

Mirko Zaffagnini , Christophe H. Marchand , M. Malferrari , Samuel Murail , Sara Bonacchi et al.

Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (51), pp.26057-26065. ⟨10.1073/pnas.1914484116⟩

Article dans une revue hal-02370717v1
Deposit thumbnail

DaReUS-Loop: a web server to model multiple loops in homology models

Yasaman Karami , Julien Rey , Guillaume Postic , Samuel Murail , Pierre Tuffery et al.

Nucleic Acids Research, 2019, 47 (W1), pp.423-428. ⟨10.1093/nar/gkz403⟩

Article dans une revue hal-03201549v1
Deposit thumbnail

Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach

Glenn Glashagen , Sjoerd de Vries , Urszula Uciechowska-Kaczmarzyk , Sergey A. Samsonov , Samuel Murail et al.

Proteins - Structure, Function and Bioinformatics, 2019, 88 (8), pp.1018-1028. ⟨10.1002/prot.25860⟩

Article dans une revue hal-03201555v1

Applications to water transport systems: general discussion

Marc Baaden , Mihail Barboiu , Manash Pratim Borthakur , Chun-Long Chen , Rob Coalson et al.

Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩

Article dans une revue hal-01926896v1

Biomimetic water channels: general discussion

Marc Baaden , Mihail Barboiu , Roslyn Bill , Chun-Long Chen , Jeffery Davis et al.

Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩

Article dans une revue hal-01926861v1
Deposit thumbnail

Water permeation across artificial I-quartet membrane channels: from structure to disorder

Samuel Murail , Tudor Vasiliu , Andrei Neamtu , Mihail Barboiu , Fabio Sterpone et al.

Faraday Discussions, 2018, 209, pp.125 - 148. ⟨10.1039/c8fd00046h⟩

Article dans une revue hal-01926847v1
Deposit thumbnail

Oriented chiral water wires in artificial transmembrane channels

Istvan Kocsis , Mirco Sorci , Heather Vanselous , Samuel Murail , Stephanie Sanders et al.

Science Advances , 2018, 4 (3), pp.eaao5603. ⟨10.1126/sciadv.aao5603⟩

Article dans une revue hal-01797309v1
Deposit thumbnail

String method solution of the gating pathways for a pentameric ligand-gated ion channel

Bogdan Lev , Samuel Murail , Frédéric Poitevin , Brett A Cromer , Marc Baaden et al.

Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (21), pp.E4158 - E4167. ⟨10.1073/pnas.1617567114⟩

Article dans une revue hal-01644525v1
Deposit thumbnail

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

Benoist Laurent , Samuel Murail , Azadeh Shahsavar , Ludovic Sauguet , Marc Delarue et al.

Structure, 2016, 24 (4), pp.595 - 605. ⟨10.1016/j.str.2016.02.014⟩

Article dans une revue hal-01400467v1
Deposit thumbnail

Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation

Erol Licsandru , Istvan Kocsis , Yue-Xiao Shen , Samuel Murail , Yves-Marie Legrand et al.

Journal of the American Chemical Society, 2016, 138 (16), pp.5403 - 5409. ⟨10.1021/jacs.6b01811⟩

Article dans une revue hal-01400466v1
Deposit thumbnail

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.

Gustavo Moraga-Cid , Ludovic Sauguet , Christèle Huon , Laurie Malherbe , Christine Girard-Blanc et al.

Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (9), pp.2865-70. ⟨10.1073/pnas.1417864112⟩

Article dans une revue hal-01230762v1

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.

Ludovic Sauguet , Frédéric Poitevin , Samuel Murail , Catherine van Renterghem , Gustavo Moraga-Cid et al.

EMBO Journal, 2013, 32 (5), pp.728-41. ⟨10.1038/emboj.2013.17⟩

Article dans une revue hal-01084646v1

Secondary and tertiary strutures of the transmembrane domains of the translocator protein TSPO determined by NMR. Stabilization of the TSPO tertiary fold upon ligand binding

S. Murail , Jc Robert , Ym Coic , Jm Neumann , Ma Ostuni et al.

Biochimica et Biophysica Acta:Biomembranes, 2008, 1778, pp.1375-81

Article dans une revue hal-00363353v1
Deposit thumbnail

Secondary and tertiary structures of the transmembrane domains of the translocator protein TSPO determined by NMR. Stabilization of the TSPO tertiary fold upon ligand binding

Samuel Murail , Jean-Claude Robert , Yves-Marie Coïc , Jean-Michel Neumann , Mariano A Ostuni et al.

Biochimica et Biophysica Acta:Biomembranes, 2008, 1778 (6), pp.1375-1381. ⟨10.1016/j.bbamem.2008.03.012⟩

Article dans une revue hal-05440360v1

Class-B GPCR activation : is ligand helix-capping the key ?

J.-M. Neumann , A. Couvineau , S. Murail , J.-J. Lacapère , N. Jamin et al.

Trends in Biochemical Sciences, 2008, 33 (7), pp.314-319. ⟨10.1016/j.tibs.2008.05.001⟩

Article dans une revue istex hal-00363367v1

The vasoactive intestinal peptide alpha helix up to C-terminus interacts with the N-terminal ectodomain of the humain VPAC1 recptor : photoaffinity, molecular modeling and dynamics.

E. Ceraudo , S. Murail , Yv Tan , Jj Lacapère , Jm Neuman et al.

Mol Endocrinol, 2008, pp.147-155

Article dans une revue hal-00258990v1
Deposit thumbnail

Characterization of the cholesterol recognition amino acid consensus sequence of the peripheral-type benzodiazepine receptor

Nadège Jamin , Jean-Michel Neumann , Mariano A. Ostuni , Thi Kim Ngoc Vu , Zhi-Xing Yao et al.

Molecular Endocrinology, 2005, 19 (3), pp.588-594. ⟨10.1210/me.2004-0308⟩

Article dans une revue hal-05324303v1
Deposit thumbnail

Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers

A Hardiagon , S Murail , L Huang , M Barboiu , F Sterpone et al.

J.M. Abadie, M., Pinteala, M., Rotaru, A. New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications, Springer, Cham., pp.51-63, 2021, 978-3-030-57455-0. ⟨10.1007/978-3-030-57456-7_3⟩

Chapitre d'ouvrage hal-02944940v1
Deposit thumbnail

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Xavier Martinez , Arthur Hardiagon , Hubert Santuz , Samuel Murail , Mihail Barboiu et al.

Lecture Notes in Bioengineering / Advances in Bionanomaterials II Selected Papers from the 3rd International Conference on Bio and Nanomaterials, BIONAM 2019, September 29 – October 3, 2019, pp.78-99, 2020, ⟨10.1007/978-3-030-47705-9_8⟩

Chapitre d'ouvrage hal-02944941v1

The modelling and enhancement of water hydrodynamics: general discussion

Marc Baaden , Manash Pratim Borthakur , Serena Casanova , Rob Coalson , Viatcheslav Freger et al.

Faraday Discussions, 209, pp.273-285, 2018, ⟨10.1039/C8FD90021C⟩

Chapitre d'ouvrage hal-02370038v1

Simulation of Ligand Binding to Membrane Proteins

Samuel Murail

Membrane Protein Structure and Function Characterization, 1635, Springer New York, pp.359-381, 2017, Methods in Molecular Biology, ⟨10.1007/978-1-4939-7151-0_20⟩

Chapitre d'ouvrage hal-04054604v1