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Article


  • 1 - 2016 ; Apr ; Licsandru, E. and Kocsis, I. and Shen, Y. X. and Murail, S. and Legrand, Y. M. and van der Lee, A. and Tsai, D. and Baaden, M. and Kumar, M. and Barboiu, M. ; Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation ; J. AM. CHEM. SOC. ; 138 ; 16 ; 5403--5409 (Google)(Scholar)(Pubmed)

  • 2 - 2016 ; Apr ; Laurent, B. and Murail, S. and Shahsavar, A. and Sauguet, L. and Delarue, M. and Baaden, M. ; Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel ; STRUCTURE ; 24 ; 4 ; 595--605 (Google)(Scholar)(Pubmed)

  • 3 - 2016 ; Jun ; Krone, M. and Kozlikova, B. and Lindow, N. and Baaden, M. and Baum, D. and Parulek, J. and Hege, H.-C. and Viola, I. ; Visual Analysis of Biomolecular Cavities: State of the Art ; COMPUTER GRAPHICS FORUM ; 35 ; 3 ; 527 - 551 (Google)(Scholar)(Pubmed)

  • 4 - 2016 ; Nov ; Kozl\'ikov\'a, B. and Krone, M. and Falk, M. and Lindow, N. and Baaden, M. and Baum, D. and Viola, I. and Parulek, J. and Hege, H.-C. ; Visualization of Biomolecular Structures: State of the Art Revisited ; COMPUTER GRAPHICS FORUM (Google)(Scholar)(Pubmed)

  • 5 - 2015 ; May ; Laurent, B. and Chavent, M. and Cragnolini, T. and Dahl, A. C. and Pasquali, S. and Derreumaux, P. and Sansom, M. S. and Baaden, M. ; Epock: rapid analysis of protein pocket dynamics ; BIOINFORMATICS ; 31 ; 9 ; 1478--1480 (Google)(Scholar)(Pubmed)

  • 6 - 2015 ; May ; Perez, S. and Tubiana, T. and Imberty, A. and Baaden, M. ; Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software ; GLYCOBIOLOGY ; 25 ; 5 ; 483--491 (Google)(Scholar)(Pubmed)

  • 7 - 2015 ; Cragnolini, T. and Doutreligne, S. and Baaden, M. and Derreumaux, P. and Pasquali, S. ; 44 Predicting and exploring complex nucleic acids architectures through a coarse-grained model ; J. BIOMOL. STRUCT. DYN. ; 33 Suppl 1 ; 30--31 (Google)(Scholar)(Pubmed)

  • 8 - 2015 ; Jun ; Cubellis, M. V. and Baaden, M. and Andreotti, G. ; Taming molecular flexibility to tackle rare diseases ; BIOCHIMIE ; 113 ; 54--58 (Google)(Scholar)(Pubmed)

  • 9 - 2015 ; Mar ; Moraga-Cid, G. and Sauguet, L. and Huon, C. and Malherbe, L. and Girard-Blanc, C. and Petres, S. and Murail, S. and Taly, A. and Baaden, M. and Delarue, M. and Corringer, P. J. ; Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure ; PROC. NATL. ACAD. SCI. U.S.A. ; 112 ; 9 ; 2865--2870 (Google)(Scholar)(Pubmed)

  • 10 - 2015 ; Mar ; Reddy, T. and Shorthouse, D. and Parton, D. L. and Jefferys, E. and Fowler, P. W. and Chavent, M. and Baaden, M. and Sansom, M. S. ; Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion ; STRUCTURE ; 23 ; 3 ; 584--597 (Google)(Scholar)(Pubmed)

  • 11 - 2014 ; May ; Oteri, F., Ciaccafava, A., Poulpiquet, A., Baaden, M., Lojou, E., Sacquin-Mora, S. ; The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes ; PHYS CHEM CHEM PHYS ; 16 ; 23 ; 11318--11322 (Google)(Scholar)(Pubmed)

  • 12 - 2014 ; Dec ; Oteri, F., Baaden, M., Lojou, E., Sacquin-Mora, S. ; 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 ; 48 ; 13800--13811 (Google)(Scholar)(Pubmed)

  • 13 - 2014 ; F. Sterpone, S. Melchionna, P. Tuffery, S. Pasquali, N. Mousseau, T. Cragnolini, Y. Chebaro, J.-F. St-Pierre, M. Kalimeri, A. Barducci, Y. Laurin, A. Tek, M. Baaden, P. Hoang Nguyen, P. Derreumaux ; The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems ; CHEMICAL SOCIETY REVIEWS ; 43 ; 13 ; 4871-4893 (Google)(Scholar)(Pubmed)

  • 14 - 2014 ; Apr ; Wang, M., Baaden, M., Wang, J., Liang, Z. ; A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450 ; J CHEM INF MODEL ; 54 ; 4 ; 1218--1225 (Google)(Scholar)(Pubmed)

  • 15 - 2014 ; Molza, A. E., Ferey, N., Czjzek, M., Le Rumeur, E., Hubert, J. F., Tek, A., Laurent, B., Baaden, M., Delalande, O. ; Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly ; FARADAY DISCUSS. ; 169 ; 45--62 (Google)(Scholar)(Pubmed)

  • 16 - 2014 ; Dreher, M., Prevoteau-Jonquet, J., Trellet, M., Piuzzi, M., Baaden, M., Raffin, B., Ferey, N., Robert, S., Limet, S. ; ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations ; FARADAY DISCUSS. ; 169 ; 119--142 (Google)(Scholar)(Pubmed)

  • 17 - 2014 ; Hirst, J. D., Glowacki, D. R., Baaden, M. ; Molecular simulations and visualization: introduction and overview ; FARADAY DISCUSS. ; 169 ; 9--22 (Google)(Scholar)(Pubmed)

  • 18 - 2013 ; Dec ; Baaden, M. and Marrink, S. J. ; Coarse-grain modelling of protein-protein interactions ; CURR. OPIN. STRUCT. BIOL. ; 23 ; 6 ; 878--886 (Google)(Scholar)(Pubmed)

  • 19 - 2013 ; Apr ; Parton, D. L. and Tek, A. and Baaden, M. and Sansom, M. S. ; Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations ; PLOS COMPUT. BIOL. ; 9 ; 4 ; e1003034 (Google)(Scholar)(Pubmed)

  • 20 - 2013 ; Lv, Z. and Tek, A. and Da Silva, F. and Empereur-mot, C. and Chavent, M. and Baaden, M. ; Game on, science - how video game technology may help biologists tackle visualization challenges ; PLOS ONE ; 8 ; 3 ; e57990 (Google)(Scholar)(Pubmed)

  • 21 - 2013 ; Mar ; Sauguet, L. and Poitevin, F. and Murail, S. and Van Renterghem, C. and Moraga-Cid, G. and Malherbe, L. and Thompson, A. W. and Koehl, P. and Corringer, P. J. and Baaden, M. and Delarue, M. ; Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels ; EMBO J. ; 32 ; 5 ; 728--741 (Google)(Scholar)(Pubmed)

  • 22 - 2013 ; Apr ; Costa, D. and Garrain, P. A. and Baaden, M. ; 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 ; 4 ; 1210--1222 (Google)(Scholar)(Pubmed)

  • 23 - 2013 ; A. Tek, M. Baaden, N. Férey, P. Bourdot ; MANHaptic: A Haptic Adaptive Method for Precise Manipulation, Assembly and Navigation ; INTERNATIONAL JOURNAL ON HUMAN MACHINE INTERACTION ; 1 ; 60-67 (Google)(Scholar)(Pubmed)

  • 24 - 2013 ; M. Dreher, M. Piuzzi, A. Turki, M. Chavent, M. Baaden, N. Férey, S. Limet, B. Raffin, S. Robert ; Interactive Molecular Dynamics: Scaling up to Large Systems. ; PROCEDIA COMPUTER SCIENCE ; 18 ; 20-29 (Google)(Scholar)(Pubmed)

  • 25 - 2012 ; April ; M. Prevost, L. Sauguet, H. Nury, C. Van Renterghem, C. Huon, F. Poitevin, M. Baaden, M. Delarue, P.-J. Corringer ; A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel ; NATURE STRUCTURAL & MOLECULAR BIOLOGY (Google)(Scholar)(Pubmed)

  • 26 - 2012 ; May ; M. Chavent, M. Baaden*, E. Hénon, S. Antonczak ; Bientôt dans votre amphithéâtre, la chimie fera son cinéma. De la bonne utilisation des ressources informatiques pour l’enseignement : visualisation moléculaire, illustration de processus chimiques et de modèles physiques ; ACTUALITé CHIMIQUE ; 363 (Google)(Scholar)(Pubmed)

  • 27 - 2012 ; June ; L. Darre, A. Tek, M. Baaden*, S. Pantano* ; Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk ; JCTC (Google)(Scholar)(Pubmed)

  • 28 - 2012 ; Nov ; B. Laurent, S. Murail, F. Da Silva, P.-J. Corringer, M. Baaden ; Modeling complex biological systems: From solution chemistry to membranes and channels ; PURE APPL. CHEM. ; ASAP (Google)(Scholar)(Pubmed)

  • 29 - 2011 ; January ; H. Nury, C. Van Renterghem, Y. Weng, A. Tran, M. Baaden, V. Dufresne, J.-P. Changeux, J. M. Sonner, M. Delarue and P.-J. Corringer ; X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel ; NATURE ; 469 ; 428–431 (Google)(Scholar)(Pubmed)

  • 30 - 2011 ; February ; M. Chavent, B. Lévy, M. Krone, K. Bidmon, J. P. Nominé, T. Ertl and M. Baaden ; GPU-powered tools boost molecular visualization ; BRIEFINGS IN BIOINFORMATICS ; 12 ; 689-701 (Google)(Scholar)(Pubmed)

  • 31 - 2011 ; Jul ; L. J. Catoire, M. Damian, M. Baaden, E. Guittet and J.-L. Banères ; Electrostatically–driven fast association and perdeuteration allow transferred cross–relaxation detection for G protein–coupled receptor ligands with equilibrium dissociation constants in the high–to–low nanomolar range ; J BIOMOLECULAR NMR ; 50 ; 3 ; 191-5 (Google)(Scholar)(Pubmed)

  • 32 - 2011 ; Oct ; M. Chavent, A. Vanel, A. Tek, B. Levy, S. Robert, B. Raffin and M. Baaden ; GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids ; J COMPUT CHEM ; 32 ; 13 ; 2924-2935 (Google)(Scholar)(Pubmed)

  • 33 - 2011 ; Sep ; O. Delalande, S. Sacquin-Mora, M. Baaden ; Enzyme closure and nucleotide binding structurally lock guanylate kinase ; BIOPHYSICAL JOURNAL ; 101 ; 6 ; 1440-1449 (Google)(Scholar)(Pubmed)

  • 34 - 2010 ; Nov ; Sacquin-Mora, S. and Delalande, O. and Baaden, M. ; Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress ; BIOPHYS J ; 99 ; 3412--3419 (Google)(Scholar)(Pubmed)

  • 35 - 2010 ; Delalande, O. and Ferey, N. and Laurent, B. and Gueroult, M. and Hartmann, B. and Baaden, M. ; Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device ; PAC SYMP BIOCOMPUT ; 205--215 (Google)(Scholar)(Pubmed)

  • 36 - 2010 ; Feb ; Corringer, P. J. and Baaden, M. and Bocquet, N. and Delarue, M. and Dufresne, V. and Nury, H. and Prevost, M. and Van Renterghem, C. ; Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues ; J. PHYSIOL. (LOND.) ; 588 ; 565--572 (Google)(Scholar)(Pubmed)

  • 37 - 2010 ; Apr ; Nury, H. and Poitevin, F. and Van Renterghem, C. and Changeux, J. P. and Corringer, P. J. and Delarue, M. and Baaden, M. ; One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue ; PROC. NATL. ACAD. SCI. U.S.A. ; 107 ; 6275--6280 (Google)(Scholar)(Pubmed)

  • 38 - 2010 ; Mar ; Sinha, D. K. and Neveu, P. and Gagey, N. and Aujard, I. and Benbrahim-Bouzidi, C. and Le Saux, T. and Rampon, C. and Gauron, C. and Goetz, B. and Dubruille, S. and Baaden, M. and Volovitch, M. and Bensimon, D. and Vriz, S. and Jullien, L. ; Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination ; CHEMBIOCHEM ; 11 ; 653--663 (Google)(Scholar)(Pubmed)

  • 39 - 2010 ; Oct ; Saladin, A. and Amourda, C. and Poulain, P. and Ferey, N. and Baaden, M. and Zacharias, M. and Delalande, O. and Prevost, C. ; Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments ; NUCLEIC ACIDS RES. ; 38 ; 6313-6323 (Google)(Scholar)(Pubmed)

  • 40 - 2010 ; Nov ; Y. Zhang, M. Baaden, J. Yan, J. Shao, S. Qiu, Y. Wu and Y. Ding ; 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 (Google)(Scholar)(Pubmed)

  • 41 - 2010 ; Nov ; M. Gueroult, D. Picot, J. Abi-Ghanem, B. Hartmann and M. Baaden ; How cations can assist DNase I in DNA binding and hydrolysis ; PLOS COMPUT. BIOL. ; 6 ; e1001000 (Google)(Scholar)(Pubmed)

  • 42 - 2009 ; Nov ; Delalande, O. and Ferey, N. and Grasseau, G. and Baaden, M. ; Complex molecular assemblies at hand via interactive simulations ; J COMPUT CHEM ; 30 ; 2375--2387 (Google)(Scholar)(Pubmed)

  • 43 - 2009 ; Jan ; Bocquet, N. and Nury, H. and Baaden, M. and Le Poupon, C. and Changeux, J. P. and Delarue, M. and Corringer, P. J. ; X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation ; NATURE ; 457 ; 111--114 (Google)(Scholar)(Pubmed)

  • 44 - 2009 ; Jul ; Durrieu, M. P. and Bond, P. J. and Sansom, M. S. and Lavery, R. and Baaden, M. ; Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states ; CHEMPHYSCHEM ; 10 ; 1548--1552 (Google)(Scholar)(Pubmed)

  • 45 - 2008 ; MAY 1 ; Durrieu, Marie-Pierre and Lavery, Richard and Baaden, Marc ; Interactions between neuronal fusion proteins explored by molecular dynamics ; BIOPHYSICAL JOURNAL ; 94 ; 9 ; 3436-3446 (Google)(Scholar)(Pubmed)

  • 46 - 2008 ; FEB ; Cox, Katherine and Bond, Peter J. and Grottesi, Alessandro and Baaden, Marc and Sansom, Mark S. P. ; Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers ; EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS ; 37 ; 2 ; 131-141 (Google)(Scholar)(Pubmed)

  • 47 - 2008 ; JAN 1 ; Neri, Marilisa and Baaden, Marc and Carnevale, Vincenzo and Anselmi, Claudio and Maritan, Amos and Carloni, Paolo ; Microseconds dynamics simulations of the outer-membrane protease T ; BIOPHYSICAL JOURNAL ; 94 ; 1 ; 71-78 (Google)(Scholar)(Pubmed)

  • 48 - 2007 ; MAR ; Tai, Kaihsu and Baaden, Marc and Murdock, Stuart and Wu, Bing and Ng, Muan Hong and Johnston, Steven and Boardman, Richard and Fangohr, Hans and Cox, Katherine and Essex, Jonathan W. and Sansom, Mark S. P. ; Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database ; JOURNAL OF MOLECULAR GRAPHICS \& MODELLING ; 25 ; 6 ; 896-902 (Google)(Scholar)(Pubmed)

  • 49 - 2005 ; OCT ; Law, RJ and Capener, C and Baaden, M and Bond, PJ and Campbell, J and Patargias, G and Arinaminpathy, Y and Sansom, MSP ; Membrane protein structure quality in molecular dynamics simulation ; JOURNAL OF MOLECULAR GRAPHICS \& MODELLING ; 24 ; 2 ; 157-165 (Google)(Scholar)(Pubmed)

  • 50 - 2004 ; DEC 1 ; Faraldo-Gomez, JD and Forrest, LR and Baaden, M and Bond, PJ and Domene, C and Patargias, G and Cuthbertson, J and Sansom, MSP ; Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations ; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS ; 57 ; 4 ; 783-791 (Google)(Scholar)(Pubmed)

  • 51 - 2004 ; NOV ; Baaden, M and Sansom, MSP ; OmpT: Molecular dynamics simulations of an outer membrane enzyme ; BIOPHYSICAL JOURNAL ; 87 ; 5 ; 2942-2953 (Google)(Scholar)(Pubmed)

  • 52 - 2003 ; AUG 1 ; Baaden, M and Meier, C and Sansom, MSP ; A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA ; JOURNAL OF MOLECULAR BIOLOGY ; 331 ; 1 ; 177-189 (Google)(Scholar)(Pubmed)

  • 53 - 2003 ; Baaden, M and Berny, F and Madic, C and Schurhammer, R and Wipff, G ; Theoretical studies on lanthanide cation extraction by picolinamides: Ligand-cation interactions and interfacial behavior ; SOLVENT EXTRACTION AND ION EXCHANGE ; 21 ; 2 ; 199-220 (Google)(Scholar)(Pubmed)

  • 54 - 2003 ; APR 8 ; Campbell, JD and Biggin, PC and Baaden, M and Sansom, MSP ; Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA ; BIOCHEMISTRY ; 42 ; 13 ; 3666-3673 (Google)(Scholar)(Pubmed)

  • 55 - 2002 ; JAN 17 ; Baaden, M and Schurhammer, R and Wipff, G ; 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 ; JOURNAL OF PHYSICAL CHEMISTRY B ; 106 ; 2 ; 434-441 (Google)(Scholar)(Pubmed)

  • 56 - 2001 ; NOV 15 ; Baaden, M and Burgard, M and Wipff, G ; TBP at the water-oil interface: The effect of TBP concentration and water acidity investigated by molecular dynamics simulations ; JOURNAL OF PHYSICAL CHEMISTRY B ; 105 ; 45 ; 11131-11141 (Google)(Scholar)(Pubmed)

  • 57 - 2001 ; FEB ; Baaden, M and Berny, F and Wipff, G ; The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation ; JOURNAL OF MOLECULAR LIQUIDS ; 90 ; 1-3, Sp. Iss. SI ; 1-9 (Google)(Scholar)(Pubmed)

  • 58 - 2001 ; Baaden, M and Burgard, M and Boehme, C and Wipff, G ; Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations ; PHYSICAL CHEMISTRY CHEMICAL PHYSICS ; 3 ; 7 ; 1317-1325 (Google)(Scholar)(Pubmed)

  • 59 - 2000 ; Troxler, L and Baaden, M and Bohmer, V and Wipff, G ; Complexation of M3+ lanthanide cations by calix[4]arene-CMPO ligands: A molecular dynamics study in methanol solution and at a water/chloroform interface ; SUPRAMOLECULAR CHEMISTRY ; 12 ; 1, Sp. Iss. SI ; 27+ (Google)(Scholar)(Pubmed)

  • 60 - 2000 ; AUG 17 ; Baaden, M and Berny, F and Madic, C and Wipff, G ; M3+ lanthanide cation solvation by acetonitrile: The role of cation size, counterions, and polarization effects investigated by molecular dynamics and quantum mechanical simulations ; JOURNAL OF PHYSICAL CHEMISTRY A ; 104 ; 32 ; 7659-7671 (Google)(Scholar)(Pubmed)

  • 61 - 2000 ; Baaden, M and Wipff, G and Yaftian, MR and Burgard, M and Matt, D ; Cation coordination by calix[4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study ; JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2 ; 7 ; 1315-1321 (Google)(Scholar)(Pubmed)

  • 62 - 2000 ; MAY 24 ; Baaden, M and Berny, F and Boehme, C and Muzet, N and Schurhammer, R and Wipff, G ; Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study ; JOURNAL OF ALLOYS AND COMPOUNDS ; 303 ; 104-111 (Google)(Scholar)(Pubmed)

  • 63 - 2000 ; MAY 15 ; Lambert, B and Jacques, V and Shivanyuk, A and Matthews, SE and Tunayar, A and Baaden, M and Wipff, G and Bohmer, V and Desreux, JF ; Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes ; INORGANIC CHEMISTRY ; 39 ; 10 ; 2033-2041 (Google)(Scholar)(Pubmed)

  • 64 - 2000 ; MAR 20 ; Baaden, M and Granger, P and Strich, A ; Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X ; MOLECULAR PHYSICS ; 98 ; 6 ; 329-342 (Google)(Scholar)(Pubmed)

    • Inproceedings


  • 1 - 2016 ; M. Trellet, N. Ferey, M. Baaden, P. Bourdot ; Interactive Visual Analytics of Molecular Data in Immersive Environments via a Semantic Definition of the Content and the Context ; IEEE VR 2016/VR 2016 Workshop on Immersive Analytics (Google)(Scholar)(Pubmed)

  • 2 - 2015 ; Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian ; Visualization of Biomolecular Structures: State of the Art ; Eurographics Conference on Visualization (EuroVis) - STARs ; R. Borgo and F. Ganovelli and I. Viola ; The Eurographics Association (Google)(Scholar)(Pubmed)

  • 3 - 2015 ; March ; S. Doutreligne and C. Gageat and T. Cragnolini and A. Taly and S. Pasquali and P. Derreumaux and M. Baaden ; UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules ; Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on ; 1-6 (Google)(Scholar)(Pubmed)

  • 4 - 2015 ; March ; M. Trellet and N. Ferey and M. Baaden and P. Bourdot ; Content and task based navigation for structural biology in 3D environments ; Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on ; 31-36 (Google)(Scholar)(Pubmed)

  • 5 - 2014 ; M. Trellet, N. Férey, M. Baaden, P. Bourdot ; Content-guided Navigation in Multimeric Molecular Complexes ; BIOIMAGING 2014 - Proceedings of the International Conference on Bioimaging, ESEO, Angers, Loire Valley, France, 3-6 March, 2014 ; 76--81 (Google)(Scholar)(Pubmed)

  • 6 - 2014 ; Nov ; S. Doutreligne and T. Cragnolini and S. Pasquali and P. Derreumaux and M. Baaden ; UnityMol: Interactive scientific visualization for integrative biology ; Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on ; 109-110 (Google)(Scholar)(Pubmed)

  • 7 - 2013 ; M. Trellet, N. Férey, M. Baaden, P. Bourdot ; Navigation guidée par le contenu pour l'exploration moléculaire. ; Actes de l'AFRV (Google)(Scholar)(Pubmed)

  • 8 - 2011 ; Matthieu Chavent, Marc Piuzzi, Alex Tek, Marc Baaden ; FvNano: A Virtual Laboratory to Manipulate Molecular Systems ; 1st IEEE symposium on biological data visualization, Providence, RI @ ieee visweek, 2011, N# 136 (Google)(Scholar)(Pubmed)

  • 9 - 2010 ; M. Chavent, A. Vanel, B. Lévy, B. Raffin, A. Tek and M. Baaden ; A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors ; JOBIM (Google)(Scholar)(Pubmed)

  • 10 - 2010 ; A. Tek, B. Laurent, N. Férey and M. Baaden ; Interacting with Molecular Simulations using a Multimodal VR Framework ; EuroVR-EVE ; 1-4 (Google)(Scholar)(Pubmed)

  • 11 - 2008 ; October ; N. Férey, O. Delalande, G. Grasseau and M. Baaden ; A VR Framework for Interacting with Molecular Simulations ; Symposium on Virtual Reality Software and Technology (ACM-VRST 2008) ; 91-94 (Google)(Scholar)(Pubmed)

  • 12 - 2008 ; November ; N. Férey, O. Delalande, G. Grasseau, and M. Baaden ; From Interactive to Immersive Molecular Dynamics ; Workshop on Virtual Reality Interaction and Physical Simulation (VRIPHYS 08 - Eurographics) ; F. Faure and M. Teschner ; 89-96 (Google)(Scholar)(Pubmed)

  • 13 - 2007 ; E. Krieger, L. Leger, M.P. Durrieu, N. Taib, P. Bond, M. Laguerre, R. Lavery, M.S.P. Sansom and M. Baaden ; Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure ; ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications ; C.B.G.R. Joubert, F. Peters, T. Lippert, M. Buecker, B. Gibbon, and B. Mohr ; John von Neumann Institute for Computing, Juelich, Germany. ; 38 ; 729-736 (Google)(Scholar)(Pubmed)

  • 14 - 2000 ; M. Baaden, F. Berny, N. Muzet, R. Schurhammer and G. Wipff ; Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores ; Proceedings of the Euradwaste 1999 conference ; C. Davies ; 390-393 (Google)(Scholar)(Pubmed)

    • Book


  • 1 - 2010 ; Collectif (M. Baaden et al.) ; Itinéraires Bis. Mon parcours de jeune chercheur : 13 chercheurs du CNRS témoignent. ; Connaissance et Savoirs (Google)(Scholar)(Pubmed)

    • Inbook


  • 1 - 2012 ; A. Tek, B. Laurent, M. Piuzzi, Z. Lu, M. Baaden, O. Delalande, M. Chavent, N. Férey, C. Martin, L. Piccinali, B. Katz, P. Bourdot, Ludovic Autin ; Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations ; W. Cai and H. Hong ; Intech, Croatia (Google)(Scholar)(Pubmed)

  • 2 - 2010 ; S. Khalid and M. Baaden ; Molecular dynamics studies of outer membrane proteins : a story of barrels ; P.C. Biggin and M.S.P. Sansom ; Royal Society of Chemistry ; 225-247 (Google)(Scholar)(Pubmed)

  • 3 - 2007 ; M. Baaden and R. Lavery ; There's plenty of room in the middle: multi-scale modelling of biological systems ; A.G. de Brevern ; Research signpost, India ; 173-195 (Google)(Scholar)(Pubmed)

  • 4 - 2000 ; M. Baaden, F. Berny, N. Muzet, L. Troxler and G. Wipff ; Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: a molecular dynamics investigation ; G. Lumetta, R.D. Rogers, and A.S. Gopalan ; Oxford University Press, New York ; 71-85 (Google)(Scholar)(Pubmed)

    • Incollection


  • 1 - 2014 ; J. Hénin, M. Baaden, A. Taly ; Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins ; Membrane Proteins Production for Structural Analysis ; Springer New York (Google)(Scholar)(Pubmed)

  • 2 - 2014 ; H\'enin, J\'er\^ome and Baaden, Marc and Taly, Antoine ; Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins ; Membrane Proteins Production for Structural Analysis ; Springer New York (Google)(Scholar)(Pubmed)

    • Phdthesis


  • 1 - 2010 ; M. Baaden ; Simulations numériques de systèmes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes (Google)(Scholar)(Pubmed)

  • 2 - 2000 ; M. Baaden ; Etudes de molécules extractantes en solution et aux interfaces liquide-liquide: aspects structuraux et mécanistiques des effets de synergie (Google)(Scholar)(Pubmed)

    • Misc


  • 1 - 2013 ; Diverse authors, M. Baaden, M. Delarue ; Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallograph (Google)(Scholar)(Pubmed)

  • 2 - 1999 ; M. Baaden ; Molecular Modeling with the ChemOffice Ultra 4.5 program suite. (Google)(Scholar)(Pubmed)

    • Poster


    Poster clippingSelective extraction of lanthanide cations by tetra-phosphineoxide substituted calix{4}arenes: a molecular dynamics study at a water/chloroform interfaceM. Baaden, M. Burgard, D. Matt et G. Wipff1999
    Poster boardDependence of isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-XA. Strich, M. Baaden et P. Granger1999
    Poster clippingComputer modeling of liquid - liquid ion extractionM. Baaden, F. Berny, N. Muzet, R. Schurhammer et G. Wipff2000
    Poster clippingEtudes de molécules extractantes en solution: aspects structuraux et mécanistiques des effets de synergieM. Baaden1999
    Poster clippingBarrels & corks in a computer, modelling bacterial iron transport systemsM. Baaden et M.S.P. Sansom2001
    Poster clippingSimulation of outer membrane proteinsM.S.P. Sansom, P. Bond, M. Baaden, J.D. Faraldo-Gómez, S. Deol, C. Meier et K. Cox2005
    Poster clippingMolecular dynamics simulations of outer membrane phospholipase AM. Baaden, C. Meier et M.S.P. Sansom2003
    Poster boardOn the convergence of the conformational sampling in molecular dynamics simulations of membrane proteinsJ.D. Faraldo-Gómez, L.R. Forrest, M. Baaden, P.J. Bond, C. Domene, G. Patargias, J. Cuthbertson et M.S.P. Sansom2005
    Poster clippingModélisation moléculaire des mutations du récepteur des lipoprotéines de faible densité impliquées dans l'hypercholesterolémie familiale au MarocR. Chater, D. Perahia, K.A. Chihab, S. Moussamih, A. Adlouni, M. Baaden, K. Zakrzewska, R. Lavery, M. El Messal et A. Kettani2005
    Poster clippingSimulation par dynamique moléculaire du complexe SNARE synaptiqueM.P. Durrieu, M. Baaden et R. Lavery2005
    Poster clippingComputational study of the low density lipoprotein receptorM. Baaden et R. Lavery2006
    Poster clippingProbing mechanical properties of molecular motors and fusion proteinsM. Baaden, M.P. Durrieu, E. Levy et R. Lavery2006
    Poster clippingFusion membranaire in silicoM.P. Durrieu, R. Lavery et M. Baaden2007
    Poster boardFlowVRNano: vers un laboratoire virtuelM. Baaden2007
    Poster clippingSHAMAN devient FlowVRNanoLBT team2008
    Poster clippingMDDriver: an efficient tool for driving Molecular Dynamics simulationsO. Delalande, N. Férey, G. Grasseau, M. Baaden2008
    Poster clippingA VR framework for interacting with molecular simulationsN. Férey, O. Delalande, G. Grasseau, M. Baaden2008
    Poster clippingSNAREs drum up in silico: molecular dynamics simulations of the synaptic fusion complexM.P. Durrieu, R. Lavery, M. Baaden2008
    Poster clippingFlowVRNano - a virtual laboratory for analysing and controlling the dynamics of molecular structuresN. Férey, O. Delalande, G. Grasseau, M. Baaden2008
    Poster clippingRelations entre fluctuations structurales et fonction enzymatique de la guanylate kinase de Mycobacterium Tuberculosis- impact de grands changements conformationnelsO. Delalande, S. Sacquin-Mora, M. Baaden2009
    Poster clippingNew insights on protein/DNA non specific interaction: the DNase I/DNA modelM. Guéroult, J, Abi Ghanem, B, Heddi, M. Lavigne, M. Baaden, B. Hartmann2009
    Poster clippingFlowVRNano - a virtual laboratory dedicated to interactive simulations of large molecular systemsN. Férey, O.Delalande, M. Baaden2009
    Poster clippingAnalyse de protéines transmembranaires par polyèdres de Voronoi/Laguerre - les canaux d´eau à travers FepAJ.Esque, M. Baaden, C. Oguey2009
    Poster clippingUsing Human Expertise in Protein-Protein Docking: From Biological Knowledge to Interactive Molecular SimulationsM. Chavent, A. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, V. Venkatraman, F. Leclerc, M. Baaden, B. Maigret,D. Ritchie2009
    Poster clippingInteractive simulations, a great promise for predicting interactionsM. Chavent, O. Delalande, N. Ferey, B. Laurent,A. Tek, M. Baaden2009
    Poster boardFlowVRNano - un laboratoire virtuel pour modéliser les systèmes moléculaires nanoscopiques en biologie et dans les matériauxN. Férey, O. Delalande, M. Baaden2009
    Poster clippingTowards efficient tools for multiscale modelling of soft matterN. Férey, O. Delalande, G. Grasseau, M. Baaden2009
    Poster clippingThe Closure Mechanism Of M. Tuberculosis Guanylate Kinase Relates Structural Fluctuations To Enzymatic FunctionO. Delalande, S. Sacquin-Mora, M. Baaden2009
    Poster clippingMulti-resolution and multi-physics approach for interactively locating funtionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic deviceO. Delalande, N. Férey, B. Laurent, M. Guéroult, B. Hartman, M. Baaden2010
    Poster clippingAugmented Dynamics : Enhanced Visualization of Molecular Dynamics TrajectoriesA. Tek, B. Laurent, M. Chavent, M. Baaden2010
    Poster clippingHigh quality visualisation: from small molecules to macromolecular systemsM. Chavent, A. Tek, A. Vanel, B. Levy, B. Raffin, M. Baaden2010
    Poster clippingA Multimodal VR Framework for Interactive Molecular SimulationsA. Tek, B. Laurent, M. Chavent, M. Baaden2010
    Poster clippingEnterobactin could play a role in preparing iron transport by remodeling the water network through FepAJ. Esque, M. Baaden, C. Oguey.2010
    Poster clippingA Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics ProcessorsM. Chavent, A. Vanel, B. Lévy, B. Raffin, A. Tek, M. Baaden2010
    Poster clippingEtude par simulation de dynamique moléculaire du complexe SNARE inséré entre deux membranesA. Tek, B. Laurent, M. Baaden2010
    Poster clippingElectrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar rangeL. J. Catoire, M. Damian, M. Baaden, E. Guittet, J.-L. Banères2011
    Poster clippingConformational dynamics in a nicotinic receptor homologue probed by simulationsH. Nury, F. Poitevin, C. Van Renterghem, B. Laurent, T. Allen, J.-P. Changeux, P.-J. Corringer, M. Delarue, M. Baaden2011
    Poster clippingFvNano - une plateforme de dynamique moléculaire interactiveM. Piuzzi, A. Tek, M. Chavent, A. Vanel, B. Raffin, A. Turki, S. Limet, S. Robert, N. Férey, M. Baaden2011
    Poster clippingUnityMol: game engine-powered GPU-boosted molecular visualizationM. Chavent, A. Tek, Z. Lv, M. Baaden2011
    Poster clippingGPU-accelerated molecular visualization using the Unity3D game engineZ. Lv, M. Chavent, A. Tek, M. Baaden2011
    Poster clippingInsights into Membrane Fusion from Molecular Dynamics Simulations of SNARE ProteinsA. Tek, B. Laurent, M. Baaden2011
    Poster clippingbioSpring, an interactive and multi-resolution software for flexible docking and for mechanical exploration of large biomolecular assemblies - methodsN. Férey, O. Delalande, M. Baaden2011
    Poster clippingFvNano - an interactive molecular dynamics platformM. Piuzzi, A. Tek, M. Baaden, M. Chavent, M. Dreher, B. Raffin, A. Turki, S. Limet, S. Robert, N. Férey2012
    Poster clippingFlowvr-Nano - visualiser, toucher, déformer et assembler des molécules du bout des doigtsM. Baaden & FvNano team2012
    Poster clippingPushing the boundaries of computational biology with interdisciplinary approachesM. Baaden2012
    Poster clippingHyperBalls on GPU: dynamic visualization of molecular structures - Scientific Visualization Accelerated by Graphics ProcessorsM. Chavent, A. Tek, Z. Lu, M. Piuzzi, B. Laurent, M. Baaden2012
    Poster clippingInsights into Membrane Fusion from Molecular Dynamics Simulations of SNARE ProteinsA. Tek, P.J. Bond, M.S.P. Sansom, M. Baaden2012
    Poster clippingStudy of the interaction between general anesthetics and a bacterial homologue to the human nicotinic receptorB. Laurent, S. Murail, P.-J. Corringer, M. Delarue, M. Baaden2012
    Poster clippingUnityMol: Visualization with a game engineZ. Lv, A. Tek, M. Chavent, M. Baaden2012

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