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Journal Article
Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW.  2017.  String method solution of the gating pathways for a pentameric ligand-gated ion channel.. Proc Natl Acad Sci U S A. 114(21):E4158-E4167.
Trellet M, Ferey N, Flotyński J, Baaden M, Bourdot P.  2018.  Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.. J Integr Bioinform. 15(2)
Martinez X, Baaden M.  2020.  Scruter les molécules en réalité virtuelle, pour quoi faire ? L'Actualité Chimique. (448):23–26.
Sauguet L., Poitevin F., Murail S., Van Renterghem C., Moraga-Cid G., Malherbe L., Thompson A.W, Koehl P., Corringer P.J, Baaden M et al..  2013.  Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Embo J.. 32:728–741.
Laurent B., Murail S., Shahsavar A., Sauguet L., Delarue M., Baaden M.  2016.  Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure. 24a:595–605.
Licsandru E., Kocsis I., Shen Y.X, Murail S., Legrand Y.M, van der Lee A., Tsai D., Baaden M, Kumar M., Barboiu M..  2016.  Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J. Am. Chem. Soc.. 138:5403–5409.
Nayeem SM, Oteri F, Baaden M, Deep S.  2017.  Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.. J Phys Chem B. 121(22):5483-5498.
Cragnolini T., Doutreligne S., Baaden M, Derreumaux P, Pasquali S..  2015.  Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure & Dynamics. 33:30–31.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
Cragnolini T., Doutreligne S., Baaden M, Derreumaux P., Pasquali S..  2015.  Predicting and exploring complex nucleic acids architectures through a coarse-grained model. J. Biomol. Struct. Dyn.. 33 Suppl 1:30–31.
Sinha D.K, Neveu P., Gagey N., Aujard I., Benbrahim-Bouzidi C., Le Saux T., Rampon C., Gauron C., Goetz B., Dubruille S. et al..  2010.  Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MSP.  2008.  Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. European Biophysics Journal with Biophysics Letters. 37:131–141.
Kocsis I, Sorci M, Vanselous H, Murail S, Sanders SE, Licsandru E, Legrand Y-M, van der Lee A, Baaden M, Petersen PB et al..  2018.  Oriented chiral water wires in artificial transmembrane channels.. Sci Adv. 4(3):eaao5603.
Sterpone F., Melchionna S., Tuffery P, Pasquali S., Mousseau N., Cragnolini T., Chebaro Y, St-Pierre J.-F., Kalimeri M., Barducci A. et al..  2014.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem. Soc. Rev.. 43:4871–4893.
Baaden M, Sansom MSP.  2004.  OmpT: Molecular dynamics simulations of an outer membrane enzyme. Biophys. J.. 87:2942–2953.
Nury H., Poitevin F., Van Renterghem C., Changeux J.P, Corringer P.J, Delarue M., Baaden M.  2010.  One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
Prevost M., Sauguet L., Nury H., Van Renterghem C., Huon C., Poitevin F., Baaden M, Delarue M., Corringer P.-J..  2012.  A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel. Nature Structural & Molecular Biology.
Reddy T., Shorthouse D., Parton D.L, Jefferys E., Fowler P.W, Chavent M, Baaden M, Sansom M.S.  2015.  Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
Sterpone F, Doutreligne S, Tran TThuy, Melchionna S, Baaden M, Nguyen PH, Derreumaux P.  2017.  Multi-scale simulations of biological systems using the OPEP coarse-grained model.. Biochem Biophys Res Commun.
Oteri F, Baaden M, Lojou E, Sacquin-Mora S.  2014.  Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J. Phys. Chem. B. 118:13800–13811.
De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A.  2019.  A molecular perspective on mitochondrial membrane fusion: from the key players to oligomerization and tethering of mitofusin. The Journal of membrane biology. 252:293–306.
Taly A, Nitti F, Baaden M, Pasquali S.  2019.  Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching. Interface focus. 9:20180065.
Martinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O'Donoghue S, Baaden M, Chavent M.  2019.  Molecular Graphics: Bridging Structural Biologists and Computer Scientists.. Structure. 27(11):1617-1623.
Baaden M, Schurhammer R, Wipff G.  2002.  Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/''oil''/TBP solutions with a comparison of supercritical CO2 and chloroform. J. Phys. Chem. B. 106:434–441.
Baaden M, Meier C, Sansom MSP.  2003.  A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA. J. Mol. Biol.. 331:177–189.