Academic Network:

• ORCID 
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Peer-reviewed scientific articles:

1. Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events.
   Stratmanm D., Moroy G.,Tufféry P and Murail S^@. ^@Corresponding Author.
   Journal of Chemical Theory and Computation (2025) In press
   DOI: 10.1021/acs.jctc.5c00950
2. Robust conformational space exploration of cyclic peptides by combining different MD protocols and force fields.
   Murail S, Sawmynaden J, Zemirli A, Jusot M, Pietrucci F, Chomilier J, Tufféry P and Stratmanm D.
   Journal of Chemical Theory and Computation (2025) 21, 19
   DOI: 10.1021/acs.jctc.5c01123
3. State-dependent dynamic communication networks in a pentameric ligand-gated ion channel.
   Lev B, Murail S, Vorobyov I, Baaden M and Allen T.
   The Journal of Physical Chemistry B (2025) 129, 37
   DOI: 10.1021/acs.jpcb.5c03991
4. Exploring the interaction between a LRRK2/PP1CA interfering peptide and PP1CA.
   Dominguez-Meijde J^*, Murail S^*, Boudjelloul R, Rebollo A and Tuffery P. ^*Contributed equally.
   Journal of Molecular Graphics and Modelling (2025) 141, 109140
   DOI: 10.1016/j.jmgm.2025.109140
5. Af-analysis: a Python package for Alphafold analysis.
   Reguei A and Murail S^@. ^@Corresponding Author.
   Journal of Open Source Software (2025) 10(107), 7577
   DOI: 10.21105/joss.07577
6. Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships.
   Ollitrault G, Achebouche R, Dreux A, Murail S, Audouze K, Tromelin A and Taboureau O.
   Nucleic Acids Research (2024) gkae305
   DOI: 10.1093/nar/gkae305
7. Exploring a structural data mining approach to design linkers for head-to-tail peptide cyclization.
   Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S and Tuffery P.
   J. Chem. Inf. Model. (2023)
   DOI: 10.1021/acs.jcim.3c00865
8. PEP-FOLD4: A pH-dependent force field for peptide structure prediction in aqueous solution.
   Rey J, Murail S, de Vries S, Derreumaux P and Tuffery P.
   Nucleic Acids Research (2023)
   DOI: 10.1093/nar/gkad376
9. In silico and in vivo studies of a tumor penetrating and interfering peptide with antitumoral effect on xenograft models of breast cancer.
   Marin G^*, Murail S^*, Andrini L, Garcia M, Loisel S, Tuffery P and Rebollo A. ^*Contributed equally.
   Pharmaceutics (2023)
   DOI: 10.3390/pharmaceutics15041180
10. Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h.
    Dorgham K^*, Murail S^*, Tuffery P, Savier E, Bravo J and Rebollo A. ^*Contributed equally.
    Pharmaceutics (2022)
    DOI: 10.3390/pharmaceutics14102055
11. An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking.
    Murail S^@, de Vries SJ, Rey J, Moroy G and Tufféry P. ^@Corresponding Author.
    Front. Mol. Biosci. (2021)
    DOI: 10.3389/fmolb.2021.716466
12. Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in a membrane-embedded artificial water channel nanoconstructs.
    Hardiagon A, Murail S, Huang LB, van der Lee A, Sterpone F, Barboiu M, Baaden M.
    J. Chem. Phys. (2021)
    DOI: 10.1063/5.0044360
13. 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.
    Quignot C, Postic G, Bret H, Rey J, Granger P, Murail S, Chacón P, Andreani J, Tuffery P, Guerois R.
    Nucleic Acids Research (2021)
    DOI: 10.1093/nar/gkab358
14. Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach.
    Glashagen G, de Vries S, Uciechowska‐Kaczmarzyk U, Samsonov SA, Murail S, Tuffery P, Zacharias M
    Proteins. (2019)
    DOI: 10.1002/prot.25860
15. Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.
    Zaffagnini M, Marchand C, Malferrari M, Murail S, Bonacchi S, Genovese S, Montalti M, Venturoli G, Falini G, Baaden M, Lemaire S, Fermani S, Trost P
    PNAS. (2019)
    DOI: 10.1073/pnas.1914484116
16. DaReUS-Loop: a web server to model loops in homology models.
    Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ
    Nucleic Acids Research (2019)
    DOI: 10.1093/nar/gkz403
17. Water permeation across artificial I-quartet membrane channels: from structure to disorder.
    Murail S^@, Vasiliu T, Neamtu A, Barboiu M, Sterpone F, Baaden M^@. ^@Corresponding Author.
    Faraday Discuss. (2018)
    DOI: 10.1039/C8FD00046H
18. Oriented chiral water wires in artificial transmembrane channels.
    Kocsis I, Sorci M, Vanselous H, Murail S, Sanders S, Licsandru E, Legrand YM, van der Lee A, Baaden M, Petersen P, Belfort G, Barboiu M
    Science Advances (2018)
    DOI: 10.1126/sciadv.aao5603
19. String method solution of the gating pathways for a pentameric ligand-gated ion channel.
    Lev B, Murail S, Poitevin F, Cromer B, Baaden M, Delarue M, Allen T
    PNAS (2017)
    F1000 recommendation.
    DOI: 10.1073/pnas.1617567114
20. Salt-excluding artificial water channels exhibiting enhanced dipolar water and proton translocation.
    Licsandru E, Kocsis I, Shen YX, Murail S, Legrand YM, van der Lee A, Tsai D, Baaden M, Kumar M, Barboiu M
    JACS (2016)
    DOI: 10.1021/jacs.6b01811
21. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel.
    Laurent B^*, Murail S^*, Shahsavar A, Sauguet L, Delarue M, Baaden M. ^*Contributed equally
    Structure (2016)
    DOI: 10.1016/j.str.2016.02.014
22. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.
    Moraga-Cid G, Sauguet L, Huon C, Malherbe L, Girard-Blanc C, Petres S, Murail S, Taly A, Baaden M, Delarue M, Corringer PJ
    PNAS (2015)
    DOI: 10.1073/pnas.1417864112
23. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.
    Sauguet L^*, Poitevin F^*, Murail S^*, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson AW, Koehl P, Corringer PJ, Baaden M, Delarue M. ^*Contributed equally.
    EMBO J (2013)
    ESRF Highlight.
    DOI: 10.1038/emboj.2013.17
24. Modeling complex biological systems: from solution chemistry to membranes and channels.
    Laurent B, Murail S, Da Silva F, Corringer PJ, Baaden M
    Pure Appl Chem (2012)
    DOI: 10.1351/PAC-CON-12-04-10
25. Molecular mechanism for the dual alcohol modulation of Cys-loop receptors.
    Murail S, Howard R, Broemstrup T, Bertaccini E, Harris RA, Trudell JR, Lindahl E
    PLoS Comput Biol (2012)
    DOI: 10.1371/journal.pcbi.1002710
26. Spatial proximity between the VPAC1 receptor and the amino terminus of agonist and antagonist peptides reveals distinct sites of interaction.
    Ceraudo E, Hierso R, Tan YV, Murail S, Rouyer-Fessard C, Nicole P, Robert JC, Jamin N, Neumann JM, Robberecht P, Laburthe M, Couvineau A
    FASEB J (2012)
    DOI: 10.1096/fj.11-196444
27. Structural basis for alcohol potentiation of a ligand-gated ion channel homolog.
    Howard R, Murail S, Ondricek KE, Corringer P-J, Lindahl E, Trudell JR, Harris RA
    PNAS (2011)
    F1000 recommendation. PSI
    Nature SBKB, featured article.
    DOI: 10.1073/pnas.1104480108
28. Microsecond Simulations Indicate that Ethanol Binds Between Subunits and Stabilizes the Open Form of a Glycine Receptor.
    Murail S, Wallner B, Trudell JR, Bertaccini E, Lindahl E
    Biophys J (2011), 100(7), 1642-50. F1000 recommendation. BJ featured article. 12th most downloaded paper of 2011 BJ.
29. Class-B GPCR activation: is ligand helix-capping the key?
    Neumann JM, Couvineau A, Murail S, Lacapère JJ, Jamin N, Laburthe M
    Trends Biochem Sci (2008), 33(7), 314-9.
30. 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.
    Murail S, Robert JC, Coïc YM, Neumann JM, Ostuni MA, Yao ZX, Papadopoulos V, Jamin N, Lacapère JJ
    BBA-Biomembranes (2008), 1778(6), 1375-81.
31. The vasoactive intestinal peptide alpha helix from Phe6 to C-terminal Asn28 interacts with the N-terminal ectodomain of the human VPAC1 receptor : photoaffinity, molecular modeling and dynamics.
    Ceraudo E, Murail S, Tan YV, Lacapere JJ, Neumann, JM, Couvineau A, Laburthe M
    Mol Endocrinology (2008), 22(1), 147-55.
32. The human VPAC1 receptor: identification of the N-terminal ectodomain as a major VIP-binding site by photoaffinity labelling and 3D modeling.
    Couvineau A, Tan YV, Ceraudo E, Lacapere JJ, Murail S, Neumann, JM, Laburthe M
    Ann N Y Acad Sci (2006), 1070, 205-9.
33. Peptide agonist docking in the N-terminal ectodomain of a class II G protein-coupled receptor, the VPAC1 receptor. Photoaffinity, NMR, and molecular modeling.
    Tan YV, Couvineau A, Murail S, Ceraudo E, Neumann JM, Lacapere JJ, Laburthe M
    J Biol Chem (2006), 281(18), 12792-8.
34. Characterization of the cholesterol recognition amino acid consensus sequence of the peripheral-type benzodiazepine receptor.
    Jamin N, Neumann JM, Ostuni MA, Vu TK, Yao ZX, Murail S, Robert JC, Giatzakis C, Papadopoulos V, Lacapere JJ
    Molecular Endocrinology (2005), 19(3), 588-94.
35. Disentangling ligand migration and heme pocket relaxation in cytochrome P450cam.
    Tetreau C, Mouawad L, Murail S, Duchambon P, Blouquit Y, Lavalette D
    Biophysical Journal (2005), 88(2), 1250-63.

Book Chapter:

1. Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers.
   Hardiagon A, Murail S, Huang L, Barboiu M, Sterpone F, Baaden M.
   New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications, Springer (2020).
2. Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels.
   Martinez X, Hardiagon A, Santuz H, Murail S, Barboiu M, Sterpone F, Baaden M..
   Advances in Bionanomaterials II. Lecture Notes in Bioengineering. Springer, Cham (2020).
3. Simulation of Ligand Binding to Membrane Proteins.
   Murail S^@. ^@Corresponding Author.
   Membrane Protein Structure and Function Characterization: Methods and Protocols. Methods Mol Biol (2017), 1635, 359–381.

Open Source Software:

1. Gromacs_py: A gromacs python wrapper.
   Murail S^@. ^@Corresponding Author.
   Zenodo (2018).
2. Docking_py, a python library for ligand protein docking.
   Tufféry P and Murail S^@. ^@Corresponding Author.
   Zenodo (2020).
3. Pdb_manip_py, a python library allowing manipulation on three-dimensional structures files (eg pdb files).
   Murail S^.
   Github.
4. Pdb-Numpy: A python library designed to facilitate working with PDB files in the context of structural bioinformatics.
   Murail S.
   Github.
5. Af-Analysis A python package for the analysis of AlphaFold protein structure predictions.
   Reguei A and Murail S^@. ^@Corresponding Author.
   Zenodo (2025).