1. El Hajj F., Fuchs P.F.J., Urbach W., Nassereddine M., Hamieh S., Taulier N. (2021)
    Molecular study of ultrasound-triggered release of fluorescein from liposomes.
    Langmuir, 37, 3868–3881. (DOI)
  2. van Gunsteren W.F.,Daura X., Fuchs P.F.J., Hansen N., Horta B.A.C., Hünenberger P.H., Mark A.E., Pechlaner M., Riniker S., Oostenbrink C. (2021)
    On the effect of the various assumptions and approximations used in molecular simulations on the properties of bio-molecular systems: overview and perspective on issues.
    ChemPhysChem, 22, 264-282. (DOI)
  3. Ostuni M.A., Hermand P., Saindoy E., Guillou N., Guellec J., Coens A., Hattab C., Desuzinges-Mandon E., Jawhari A., Iatmanen-Harbi S., Lequin O., Fuchs P.F.J., Lacapère J.-J., Combadière C., Pincet F., Deterre P. (2020)
    CX3CL1 homo-oligomerization drives cell-to-cell adherence.
    Scientific Reports, 10, 9069. (DOI)
  4. Jobin M.-L., Vamparys L., Deniau R., Grélard A., Mackereth C.D., Fuchs P.F.J., Alves I.D. (2019)
    Biophysical Insight on the Membrane Insertion of an Arginine-Rich Cell-Penetrating Peptide.
    International Journal of Molecular Sciences, 20, 4441. (DOI)
  5. Gonçalves Y., Senac C., Fuchs P.F.J., Hünenberger P., Horta B. (2019)
    Influence of the treatment of non-bonded interactions on thermodynamic and transport properties of pure liquids calculated using the 2016H66 force field.
    Journal of Chemical Theory and Computation, 15, 1806-1826. (DOI)
  6. Gautier R., Bacle A., Tiberti M.L., Fuchs P.F.J., Vanni S. , Antonny B. (2018)
    PackMem: a versatile tool to compute and visualize interfacial packing defects in lipid bilayers.
    Biophysical Journal, 115, 436-444. (DOI)
    The Packmem program is avalaible on github. We also have a PackMem website with advices and tutorials.
  7. Daste F., Sauvanet C., Bavdek A., Baye J., Pierre F., Le Borgne R., David C., Rojo R., Fuchs P.F.J., Tareste D. (2018)
    The heptad repeat domain 1 of Mitofusin has membrane destabilization function in mitochondrial fusion.
    EMBO reports, 19, e43637.(DOI)
  8. Abdollahi N., Albani A., Anthony E., Baud A., Cardon M., Clerc R., Czernecki D., Conte R., David L., Delaune A., Djerroud S., Fourgoux P., Guiglielmoni N., Laurentie J., Lehmann N., Lochard C., Montagne R., Myrodia V., Opuu V., Parey E., Polit L., Privé S., Quignot C., Ruiz-Cuevas M., Sissoko M., Sompairac N., Vallerix A., Verrecchia V., Delarue M., Guérois R., Ponty Y., Sacquin-Mora S., Carbone A., Froidevaux C., Le S., Lespinet O., Weigt M., Abboud S., Bernardes J., Bouvier G., Dequeker C., Ferré A., Fuchs P.F.J, Lelandais G., Poulain P., Richard H., Schweke H., Laine E., Lopes A. (2018)
    Meet-U: Educating through research immersion.
    PLOS Computational Biology, 14, e1005992.(DOI)
  9. Senac C., Desgranges S., Contino-Pépin C., Urbach W., Fuchs P.F.J., Taulier N. (2018)
    Effect of dimethyl sulfoxide on the binding of 1-adamantane carboxylic acid to beta- and gamma-cyclodextrins.
    ACS Omega, 3, 1014-1021.(DOI)
  10. Senac C., Urbach W., Kurtisovski E., Hunenberger P., Horta B., Taulier N., Fuchs P.F.J. (2017)
    Simulating bilayers of nonionic surfactants with the GROMOS-compatible 2016H66 force field.
    Langmuir, 33,10225–10238.(DOI).
    The parameters used in this paper are accessible on github.
  11. Bacle A., Gautier R., Jackson C.L., Fuchs P.F.J.*, Vanni S.* (2017)
    Interdigitation between core triglycerides and surface phospholipids modulates the surface properties of lipid droplets.
    Biophysical Journal, 112, 1417-1430.(DOI).
    * both authors contributed equally. The parameters and scripts used in this paper are accessible on github.
  12. Horta B.A.C., Merz P.T., Fuchs P.F.J., Dolenc J., Riniker S., Hunenberger P.H. (2016)
    A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set.
    Journal of Chemical Theory and Computation, 12, 3825-3850.(DOI)
  13. Ferru-Clement R., Spanova M., Dhayal S., Morgan N.G., Helye R., Becq F, Hirose H., Antonny B., Vamparys L., Fuchs P.F.J, Ferreira T. (2016)
    Targeting surface voids to counter membrane disorders in lipointoxication-related diseases.
    Journal of Cell Science, 129, 2368-2381.(DOI)
  14. Botan A., Favela F., Fuchs P.F.J., Javanainen M., Kanduc M., Kulig W., Lamberg A., Loison C., Lyubartsev A., Miettinen M., Monticelli L., Maatta J., Ollila S., Retegan M., Rog T., Santuz H., Tynkkynen J.P. (2015)
    Towards Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.
    The Journal of Physical Chemistry B, 119, 15075-15088.(DOI)
  15. Floch A.G., Tareste D., Fuchs P.F.J., Chadrin A., Naciri I., Leger T., Schlenstedt G., Palancade B., Doye V. (2015)
    Nuclear pore targeting of the yeast Pom33 nucleoporin depends on karyopherin- and lipid-binding.
    Journal of Cell Science, 128, 305-316.(DOI)
  16. Jallu V., Poulain P., Fuchs P.F.J., Kaplan C., de Brevern A.G. (2014)
    Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit .3: structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants.
    Biochimie, 105, 84-90.(DOI)
  17. Charlier L., Louet M., Chaloin L., Fuchs P.F.J, Martinez J., Muriaux D., Favard C., Floquet N. (2014)
    Coarse Grained Simulations of the HIV-1 Matrix Protein Anchoring: revisiting its assembly on membrane domains.
    Biophysical Journal, 106, 577-585.(DOI)
  18. Manoharan M., Fuchs P.F.J., Ramanathan S., Offmann B. (2013)
    Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations.
    Journal of Biomolecular Structure and Dynamics, 32, 1742-1751.(DOI)
  19. Vamparys L., Gautier R., Vanni S., Bennett W.F.D., Tieleman D.P., Antonny B., Etchebest C., Fuchs P.F.J. (2013)
    Conical lipids in flat bilayers induce packing defects similar to that induced by positive curvature.
    Biophysical Journal, 104, 585-593.(DOI)
        This paper is commented by G. Voth: DOI.
  20. Vanni S., Vamparys L., Gautier R., Drin G., Etchebest C., Fuchs P.F.J., Antonny B. (2013)
    Amphipathic Lipid Packing Sensor Motifs: Probing Bilayer Defects with Hydrophobic Residues.
    Biophysical Journal, 104, 575-584.(DOI)
        This paper is commented by G. Voth: DOI.
  21. Rossi G., Fuchs P.F.J., Barnoud J., Monticelli L. (2012)
    A Coarse-Grained Martini Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants.
    The Journal of Physical Chemistry B, 116, 14353.14362.(DOI)
  22. Jallu V.#, Poulain P.#, Fuchs P.F.J., Kaplan C., de Brevern A.G. (2012)
    Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the beta3 Subunit of the aIIbeta3 Integrin.
    PLOS ONE, 7, e47304.(DOI)
    # These authors contributed equally to this work.
  23. Fuchs P.F.J., Hansen H.S., Hunenberger P.H., Horta B.A.C. (2012)
    A GROMOS parameter set for vicinal diether functions: properties of polyethyleneoxide and polyethyleneglycol.
    Journal of Chemical Theory and Computation, 8, 3943-3963. (DOI)
  24. Gonzalez-Rubio P., Gautier R., Etchebest C., Fuchs P.F.J. (2011)
    Amphipathic-Lipid-Packing-Sensor interactions with lipids assessed by atomistic molecular dynamics.
    BBA Biomembranes, 1808, 2119-2127.(DOI)
  25. Horta B.A.C, Fuchs P.F.J., van Gunsteren W.F., Hunenberger P.H. (2011)
    New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters.
    Journal of Chemical Theory and Computation, 7, 1016-1031.(DOI)
  26. Monticelli L., Tieleman D.P, Fuchs P.F.J. (2010)
    Interpretation of 2H-NMR Experiments on the Orientation of the Transmembrane Helix WALP23 by Computer Simulations.
    Biophysical Journal, 99, 1455-1464.(DOI)
  27. Fuchs P.F.J. (2010)
    Molecular dynamics of membrane peptides and proteins: principles and comparison to experimental data. Methods in Molecular Biology (Volume 654, Part 5) / Edited by J.-J. Lacapère, Humana Press Inc. Totowa, NJ, USA , pp 403-421.(DOI)
  28. Özdirekcan S., Etchebest C., Killian J.A., Fuchs P.F.J. (2007)
    On the orientation of a designed transmembrane peptide: towards the right tilt angle?
    Journal of the American Chemical Society,129, 15174 -15181.(DOI)
  29. Fuchs P.F.J., Etchebest C., de Brevern A.G. (2007)
    Turns prediction.
    In: Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India. (Ed.), 43-63.(abstract)
  30. Fuchs P.F.J., Bonvin A.M.J.J., Bochicchio B., Pepe A., Alix A.J.P., Tamburro A.M. (2006)
    Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR and microsecond explicit molecular dynamics study of the GDNP tetrapeptide.
    Biophysical Journal, 90, 2745-2759.(DOI)
  31. Fuchs P.F.J., Alix A.J.P. (2005)
    High accuracy prediction of beta-turns and their types using propensities and multiple alignments.
    Proteins: Structure, Function, Bioinformatics, 59, 828-839.(DOI)
    COUDES can be used as a web-service on the RPBS platform.
  32. Tzakos A., Fuchs P.F.J., van Nuland N., Troganis A., Tselios T., Deraos S., Matsoukas J., Gerothanassis I., Bonvin A.M.J.J. (2004)
    NMR and MD Studies of an Autoimmune MBP Peptide and its Antagonist. Structural Implications for the MHC II (I-Au) - Peptide Complex through Docking Calculations.
    European Journal of Biochemistry, 271, 3399-3413. (DOI)
  33. Alix A.J.P., Bochicchio B., Dauchez M., Debelle L., Derreumaux P., Floquet N., Fuchs P.F.J, Héry S., Kaplan H., Moroy G., Tamburro A.M. (2003)
    Elastin in silico.
    In: Elastin 2002, Eds. Tamburro A.M. and Pepe A., EditricErmes, Potenza (Italy), 15-30.(book)
  34. Fuchs P.F.J., Bochicchio B., Pepe A., Bonvin A., Alix A.J.P, Tamburro A.M. (2003)
    Spectroscopic and theoritical characterization of type VIII beta-turn. Study of the tetrapeptide GDNP.
    In: Elastin 2002, Eds. Tamburro A.M. and Pepe A., EditricErmes, Potenza (Italy), 81-88.(book)
  35. Fuchs P.F.J., Segalas I., Toma F., Alix A.J.P. (2001)
    Spectroscopic Structural Study of the R2 Repetition of the c-Myb Transcription Factor.
    Journal of Molecular Structure, 563-564, 111-114. (DOI)
  36. Fuchs P.F.J., Debelle L., Alix A.J.P. (2001)
    Structural Study of some Specific Elastin Hexapeptides Activating MMP1.
    Journal of Molecular Structure, 565-566, 335-339. (DOI)
  37. Brassart B., Fuchs P.F.J., Huet E., Alix A.J.P., Wallach J., Tamburro A.M., Delacoux F., Haye B., Hemonard H., Hornebeck W., Debelle L. (2001)
    Conformational Dependance of MMP1 Up-Regulation by Elastin Peptides in Cultured Fibroblasts.
    Journal of Biological Chemistry, 276, 5222-5227. (DOI)

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