Publications

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Journal Article
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)
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.
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.
Cubellis M.V, Baaden M, Andreotti G..  2015.  Taming molecular flexibility to tackle rare diseases. Biochimie. 113:54–58.
Zhang Y., Baaden M, Yan J., Shao J., Qiu S., Wu Y., Ding Y..  2010.  The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif. J. Phys. Chem. B. 114:13839–13846.
Oteri F, Ciaccafava A, Poulpiquet A, Baaden M, Lojou E, Sacquin-Mora S.  2014.  The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys. Chem. Chem. Phys.. 16:11318–11322.
Perez S., Tubiana T., Imberty A., Baaden M.  2015.  Three-dimensional representations of complex carbohydrates and polysaccharides–SweetUnityMol: a video game-based computer graphic software. Glycobiology. 25:483–491.
Baaden M, Burgard M, Wipff G.  2001.  TBP at the water-oil interface: The effect of TBP concentration and water acidity investigated by molecular dynamics simulations. J. Phys. Chem. B. 105:11131–11141.
Baaden M, Berny F, Madic C, Schurhammer R, Wipff G.  2003.  Theoretical studies on lanthanide cation extraction by picolinamides: Ligand-cation interactions and interfacial behavior. Solvent Extr. Ion Exch.. 21:199–220.
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.
Corringer P.J, Baaden M, Bocquet N., Delarue M., Dufresne V., Nury H., Prevost M., Van Renterghem C..  2010.  Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J. Physiol. (lond.). 588:565–572.
Costa D., Garrain P.A, Baaden M.  2013.  Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. J. Biomed. Mater. Res. A. 101:1210–1222.
Krone M., Kozlikova B., Lindow N., Baaden M, Baum D., Parulek J., Hege H.-C., Viola I..  2016.  Visual Analysis of Biomolecular Cavities: State of the Art. Comput. Graphics Forum. 35:527–551.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2017.  Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures. Computer Graphics Forum. 36:178–204.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2016.  Visualization of Biomolecular Structures: State of the Art Revisited. Comput. Graphics Forum.
Baaden M.  2019.  Visualizing Biological Membrane Organization and Dynamics.. J Mol Biol. 431(10):1889-1919.
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.
Martinez X, Chavent M, Baaden M.  2020.  Visualizing protein structures - tools and trends.. Biochem Soc Trans.
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.
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.
Bocquet N., Nury H., Baaden M, Le Poupon C., Changeux J.P, Delarue M., Corringer P.J.  2009.  X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature. 457:111–114.
Nury H., Van Renterghem C., Weng Y., Tran A., Baaden M, Dufresne V., Changeux J.-P., Sonner J.M, Delarue M., Corringer P.-J..  2011.  X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469:428–431.

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