Publications

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Journal Article
Mazzanti L, Doutreligne S, Gageat C, Derreumaux P, Taly A, Baaden M, Pasquali S.  2017.  What Can Human-Guided Simulations Bring to RNA Folding? Biophys J. 113(2):302-312.
Murail S, Vasiliu T, Neamtu A, Barboiu M, Sterpone F, Baaden M.  2018.  Water permeation across artificial I-quartet membrane channels: from structure to disorder.. Faraday Discuss. 209:125-148.
Martinez X, Chavent M, Baaden M.  2020.  Visualizing protein structures - tools and trends.. Biochem Soc Trans.
Laureanti J, Brandi J, Offor E, Engel D, Rallo R, Ginovska B, Martinez X, Baaden M, Baker NA.  2020.  Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.. Protein Sci. 29(1):237-246.
Baaden M.  2019.  Visualizing Biological Membrane Organization and Dynamics.. J Mol Biol. 431(10):1889-1919.
Tai K, Baaden M, Murdock S, Wu B, Ng MHong, Johnston S, Boardman R, Fangohr H, Cox K, Essex JW et al..  2007.  Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database. Journal of Molecular Graphics \& Modelling. 25:896–902.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.. Data Brief. 26:104460.
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.
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.
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.
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, 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.
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.
Brandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F.  2019.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports. 9:16450.
Brandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F.  2019.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.. Sci Rep. 9(1):16450.
Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M.  2018.  MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.. J Integr Bioinform. 15(2)
Neri M, Baaden M, Carnevale V, Anselmi C, Maritan A, Carloni P.  2008.  Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J.. 94:71–78.
De Vecchis D, Cavellini L, Baaden M, Hénin J, Cohen MM, Taly A.  2017.  A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep. 7(1):10217.
Röper J-C, Mitrossilis D, Stirnemann G, Waharte F, Brito I, Fernandez-Sanchez M-E, Baaden M, Salamero J, Farge E.  2018.  The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation .. Elife. 7

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