The publication list below is dynamically generated by the French archive HAL and also links to the full texts when possible. If you are looking for something specific and want to search the abstracts of my publications, go to this page. This listing systematically provides the corresponding BibTex citation. My current open access score derived from my ORCID entry page is 58% with 74 open access and 54 closed access. Note that the HAL archive contains a more complete coverage of both my publications in general and openly accessible full texts, including for instance author-generated versions of some articles. Alternatively, you can consult my Google Scholar profile here or visit my ResearchGate page here.
There is also a dedicated page listing all published datasets with their digital object identifiers (DOI) and URLs here. If you are interested in the scientific posters I have contributed to, please visit my Scientific Posters page.
The only thing more tedious than writing a scientific paper is reading one.
Publications HAL
2024
Journal articles
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Raphaëlle Versini, Marc Baaden, Laetitia Cavellini, Mickaël M Cohen, Antoine Taly, et al.. Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion. Structure, 2024, 32 (11), pp.1997-2012.e7. ⟨10.1101/2023.09.22.559002⟩. ⟨hal-04299450⟩
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Marc Baaden. MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform. Journal of Physical Chemistry B, 2024, 128 (38), pp.9132-9142. ⟨10.1021/acs.jpcb.4c04712⟩. ⟨hal-04794544⟩
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Hayet Belghit, Mariano Spivak, Manuel Dauchez, Marc Baaden, Jessica Jonquet-Prevoteau. From complex data to clear insights: visualizing molecular dynamics trajectories. Frontiers in Bioinformatics, 2024, 4, ⟨10.3389/fbinf.2024.1356659⟩. ⟨hal-04568346⟩
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Conference papers
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Rajkumar Darbar, Hubert Santuz, Antoine Taly, Marc Baaden. GazeMolVR: Sharing Eye-Gaze Cues in a Collaborative VR Environment for Molecular Visualization. International Conference on Mobile and Ubiquitous Multimedia (MUM '24), December 1--4, 2024, Stockholm, Sweden, Dec 2024, Stockholm (Suède), Sweden. ⟨10.1145/3701571.3701599⟩. ⟨hal-04794567⟩
Marc Baaden, Fabio Sterpone, Antoine Taly. 5. Les supercalculateurs et l'intelligence artificielle révèlent le monde moléculaire. Le calcul pour les Big Data et l’Intelligence Artificielle, pp.138-141, A paraître. ⟨hal-04799896⟩
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2023
Journal articles
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David Kuťák, Pere‐pau Vázquez, Tobias Isenberg, Michael Krone, Marc Baaden, et al.. State of the Art of Molecular Visualization in Immersive Virtual Environments. Computer Graphics Forum, 2023, 42 (6), pp.e14738:1--e14738:29. ⟨10.1111/cgf.14738⟩. ⟨hal-04006531⟩
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Li-Bo Huang, Fumihiko Mamiya, Marc Baaden, Eiji Yashima, Mihail Barboiu. Self-Assembling Peptide-Appended Metallomacrocycle Pores for Selective Water Translocation. ACS Applied Materials & Interfaces, 2023, 15 (33), pp.40133-40139. ⟨10.1021/acsami.3c09059⟩. ⟨hal-04257762⟩
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Robin A Corey, Marc Baaden, Matthieu Chavent. A brief history of visualizing membrane systems in molecular dynamics simulations. Frontiers in Bioinformatics, 2023, 3, pp.1149744. ⟨10.3389/fbinf.2023.1149744⟩. ⟨hal-04306431⟩
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Johanna K S Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, et al.. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. eLife, 2023, ⟨10.7554/elife.90061⟩. ⟨hal-04254566v2⟩
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André Lanrezac, Marc Baaden. UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. Membranes, 2023, 13 (3), pp.362. ⟨10.3390/membranes13030362⟩. ⟨hal-04306427⟩
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Yubo Zhang, Marc Baaden. Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT. Catalysts, 2023, 13 (2), pp.214. ⟨10.3390/catal13020214⟩. ⟨hal-03943290⟩
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Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas, Thibault Tubiana, Sana Zineb Aimeur, et al.. A Perspective on the prospective use of AI in protein structure prediction. Journal of Chemical Information and Modeling, 2023, 64 (1), pp.26-41. ⟨10.1021/acs.jcim.3c01361⟩. ⟨hal-04306436⟩
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Iuliana‐marilena Andrei, Dmytro Strilets, Shixin Fa, Marc Baaden, Tomoki Ogoshi, et al.. Combinatorial Screening of Water/Proton Permeation of Self‐Assembled Pillar[5]arene Artificial Water Channel Libraries. Angewandte Chemie International Edition, 2023, 62 (42), pp.e202310812. ⟨10.1002/anie.202310812⟩. ⟨hal-04257786⟩
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Iuliana M Andrei, Wenzhang Chen, Marc Baaden, Stéphane P Vincent, Mihail Barboiu. Proton- versus Cation-Selective Transport of Saccharide Rim-Appended Pillar[5]arene Artificial Water Channels. Journal of the American Chemical Society, 2023, 145 (40), pp.21904-21914. ⟨10.1021/jacs.3c06335⟩. ⟨hal-04257737⟩
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Iuliana Andrei, Wenzhang Chen, Marc Baaden, Stéphane Vincent, Mihail Barboiu. Proton versus cation selective transport of saccharide rim-appended pillar[5]arene PA-S artificial water channels. Journal of the American Chemical Society, 2023, 145 (40), pp.21904-21914. ⟨10.1021/jacs.3c06335⟩. ⟨hal-04742187⟩
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Poster communications
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Laetitia Cavellini, Maria de los Ángeles Morcillo Parra, Antoine Taly, Marc Baaden, Mickael M. Cohen. Structure-Function analysis of the yeast mitofusin Fzo1. 22ème congrès du Groupe Français de Bioenergetique, Sep 2023, Bedoin, France. ⟨hal-04466677⟩
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Sophie Sacquin-Mora, Nicolas Bourassin, Florent Barbault, Marc Baaden. Between two walls: Modeling the adsorption behavior of redox enzymes on bare and SAM-functionalised gold surfaces. XXIIIème congrès du GGMM, May 2023, Toulouse, France. ⟨hal-04112652⟩
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Preprints, Working Papers, ...
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Staëlle Makamte, Amira Jabrani, Annick Paquelin, Anne Plessis, Mathieu Sanial, et al.. A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study. 2023. ⟨hal-04019989⟩
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2022
Journal articles
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André Lanrezac, Benoist Laurent, Hubert Santuz, Nicolas Férey, Marc Baaden. Fast and Interactive Positioning of Proteins within Membranes. Algorithms, 2022, 15 (11), pp.415. ⟨10.3390/a15110415⟩. ⟨hal-03873725⟩
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Arthur Hardiagon, Marc Baaden, Fabio Sterpone. Artificial Water Channels Form Precursors to Sponge-Like Aggregates in Water–Ethanol Mixtures. Journal of Physical Chemistry A, 2022, 126 (38), pp.6628-6636. ⟨10.1021/acs.jpca.2c04545⟩. ⟨hal-03873715⟩
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Marc Baaden. Deep inside molecules - digital twins at the nanoscale. Virtual Reality & Intelligent Hardware, 2022, 4, pp.324 - 341. ⟨10.1016/j.vrih.2022.03.001⟩. ⟨hal-03873710⟩
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Björn Sommer, Daisuke Inoue, Marc Baaden. Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design. Journal of Integrative Bioinformatics, 2022, 19 (2), ⟨10.1515/jib-2022-0037⟩. ⟨hal-03873706⟩
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Nicolas Bourassin, Florent Barbault, Marc Baaden, Sophie Sacquin-Mora. Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces. Langmuir, 2022, 38 (4), pp.1313-1323. ⟨10.1021/acs.langmuir.1c01774⟩. ⟨hal-03294641⟩
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Staëlle Makamte, Aurélien Thureau, Amira Jabrani, Annick Paquelin, Anne Plessis, et al.. A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study. Journal of Structural Biology, 2022, 214 (2), pp.107853. ⟨10.1016/j.jsb.2022.107853⟩. ⟨hal-03413156⟩
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Anne-Elisabeth Molza, Yvonne Westermaier, Magali Moutte, Pierre Ducrot, Claudia Danilowicz, et al.. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences, 2022, 9, pp.826136. ⟨10.3389/fmolb.2022.826136⟩. ⟨hal-03826944⟩
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Davide Spalvieri, Anne-Marine Mauviel, Matthieu Lambert, Nicolas Férey, Sophie Sacquin-Mora, et al.. Design – a new way to look at old molecules. Journal of Integrative Bioinformatics, 2022, 19 (2), pp.20220020. ⟨10.1515/jib-2022-0020⟩. ⟨hal-03793308⟩
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Conference papers
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F. Cailliez, Xiaojing Wu, Jérôme Hénin, Laura Baciou, Marc Baaden, et al.. Simulation moléculaire du transfert d’électron transmembranaire dans NOX5. 3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France. ⟨hal-04426169⟩
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2021
Journal articles
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Núria López, Luigi del Debbio, Marc Baaden, Matej Praprotnik, Laura Grigori, et al.. Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (46), pp.e2024891118. ⟨10.1073/pnas.2024891118⟩. ⟨hal-03438495⟩
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Marc Baaden. The never-ending quest to understand the shapes and motions of molecules. The Biochemist, 2021, 43 (5), pp.22-24. ⟨10.1042/bio_2021_175⟩. ⟨hal-03438490⟩
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Xavier Martinez, Marc Baaden. UnityMol prototype for FAIR sharing of molecular- visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments. Acta crystallographica Section D : Structural biology [1993-..], 2021, 77 (6), pp.746-754. ⟨10.1107/S2059798321002941⟩. ⟨hal-02944943v2⟩
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Arthur Hardiagon, Samuel Murail, Li-Bo Huang, Arie van Der Lee, Fabio Sterpone, et al.. Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs. The Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩. ⟨hal-03410227⟩
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Xiaojing Wu, Jérôme Hénin, Laura Baciou, Marc Baaden, Fabien Cailliez, et al.. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations. Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩. ⟨hal-03382660⟩
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André Lanrezac, Nicolas Férey, Marc Baaden. Wielding the power of interactive molecular simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021, 12 (4), pp.e1594. ⟨10.1002/WCMS.1594⟩. ⟨hal-03447181⟩
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Li-Bo Huang, Arthur Hardiagon, Istvan Kocsis, Cristina-Alexandra Jegu, Mihai Deleanu, et al.. Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation. Journal of the American Chemical Society, 2021, 143 (11), pp.4224-4233. ⟨10.1021/jacs.0c11952⟩. ⟨hal-03364954v2⟩
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Book sections
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A Hardiagon, S Murail, L Huang, M Barboiu, F Sterpone, et al.. Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers. J.M. Abadie, M., Pinteala, M., Rotaru, A. New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications, Springer, Cham., pp.51-63, 2021, 978-3-030-57455-0. ⟨10.1007/978-3-030-57456-7_3⟩. ⟨hal-02944940⟩
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Marc Baaden, Emmanuel Maisonhaute. Voir et manipuler les molécules. Du virtuel au réel. C.M. Pradier, O. Parisel, F. Teyssandier. Etonnante chimie. Découvertes et promesses du XXIè siècle, CNRS Editions, pp.182-187, 2021, 978-2-271-13652-7. ⟨hal-03211883⟩
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2020
Journal articles
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Nicolas Bourassin, Marc Baaden, Elisabeth Lojou, Sophie Sacquin-Mora. Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grain Representation. Journal of Physical Chemistry B, 2020, 15, ⟨10.1021/acs.jpcb.0c05347⟩. ⟨hal-02939019⟩
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Xavier Martinez, Matthieu Chavent, Marc Baaden. Visualizing protein structures - tools and trends. Biochemical Society Transactions, 2020, 48 (2), pp.499-506. ⟨10.1042/BST20190621⟩. ⟨hal-02946006⟩
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Xavier Martinez, Marc Baaden. Scruter les molécules en réalité virtuelle, pour quoi faire ?. L'Actualité Chimique, 2020, 448, pp.23-26. ⟨hal-02946000⟩
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Joseph Laureanti, Juan Brandi, Elvis Offor, David Engel, Robert Rallo, et al.. Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS. Protein Science, 2020, 29 (1), pp.237-246. ⟨10.1002/pro.3773⟩. ⟨hal-02370955⟩
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Mattia Migliore, Andrea Bonvicini, Vincent Tognetti, Laure Guilhaudis, Marc Baaden, et al.. Characterization of β-turns by electronic circular dichroism spectroscopy: A coupled molecular dynamics and time-dependent density functional theory computational study. Physical Chemistry Chemical Physics, 2020, 22 (3), pp.1611-1623. ⟨10.1039/C9CP05776E⟩. ⟨hal-02397135⟩
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Dmytro Strilets, Shixin Fa, Arthur Hardiagon, Marc Baaden, Tomoki Ogoshi, et al.. Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers. Angewandte Chemie International Edition, 2020, 59 (51), pp.23213-23219. ⟨10.1002/anie.202009219⟩. ⟨hal-03028876⟩
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Book sections
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Marc Baaden. Computer Simulations Provide Guidance for Molecular Medicine through Insights on Dynamics and Mechanisms at the Atomic Scale. In: Van Toi V., Le T., Ngo H., Nguyen TH. (eds). 7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7) Translational Health Science and Technology for Developing Countries, 69, Springer, pp.261-265, 2020, IFMBE Proceedings, ⟨10.1007/978-981-13-5859-3_47⟩. ⟨hal-02370021⟩
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Xavier Martinez, Arthur Hardiagon, Hubert Santuz, Samuel Murail, Mihail Barboiu, et al.. Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels. Lecture Notes in Bioengineering / Advances in Bionanomaterials II Selected Papers from the 3rd International Conference on Bio and Nanomaterials, BIONAM 2019, September 29 – October 3, 2019, pp.78-99, 2020, ⟨10.1007/978-3-030-47705-9_8⟩. ⟨hal-02944941⟩
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2019
Journal articles
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Astrid F. Brandner, Stepan Timr, Simone Melchionna, Philippe Derreumaux, Marc Baaden, et al.. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports, 2019, 9, pp.16450. ⟨10.1038/s41598-019-52760-y⟩. ⟨hal-02370975⟩
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Astrid Brandner, Dario de Vecchis, Marc Baaden, Mickaël M Cohen, Antoine Taly. Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion, 2019, 49, pp.234-244. ⟨10.1016/j.mito.2019.06.010⟩. ⟨hal-02345043⟩
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Xavier Martinez, Michael Krone, Naif Alharbi, Alexander Rose, Robert Laramee, et al.. Molecular Graphics: Bridging Structural Biologists and Computer Scientists. Structure, 2019, 27 (11), pp.1617-1623. ⟨10.1016/j.str.2019.09.001⟩. ⟨hal-02370947⟩
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Antoine Taly, F. Nitti, Marc Baaden, S. Pasquali. Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching. Interface Focus, 2019, 9 (3), pp.20180065. ⟨10.1098/rsfs.2018.0065⟩. ⟨hal-02345057⟩
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Marc Baaden. Visualizing Biological Membrane Organization and Dynamics. Journal of Molecular Biology, 2019, 431 (10), pp.1889-1919. ⟨10.1016/j.jmb.2019.02.018⟩. ⟨hal-02370047⟩
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Dario de Vecchis, Astrid Brandner, Marc Baaden, Mickaël M Cohen, Antoine Taly. A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin. Journal of Membrane Biology, 2019, 252 (4-5), pp.293-306. ⟨10.1007/s00232-019-00089-y⟩. ⟨hal-02345040⟩
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Astrid Brandner, Dario de Vecchis, Marc Baaden, Mickaël M Cohen, Antoine Taly. Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking. Data in Brief, 2019, 26, pp.104460. ⟨10.1016/j.dib.2019.104460⟩. ⟨hal-02345034⟩
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Mirko Zaffagnini, Christophe H. Marchand, M. Malferrari, Samuel Murail, Sara Bonacchi, et al.. Glutathionylation primes soluble GAPDH for late collapse into insoluble aggregates. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (51), pp.26057-26065. ⟨10.1073/pnas.1914484116⟩. ⟨hal-02370717⟩
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Conference papers
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Xavier Martinez, Michael Krone, Marc Baaden. QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces. MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2019, Jun 2019, Porto, Portugal. ⟨10.2312/molva.20191095⟩. ⟨hal-02370900⟩
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Proceedings
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Mihail Barboiu, Manish Kumar, Marc Baaden, Philip Gale, Bruce Hinds. Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK. Chemical Communications, 55 (27), pp.3853-3858, 2019, ⟨10.1039/c9cc90112d⟩. ⟨hal-02127512⟩
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2018
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Jeremy Esque, Mark S. P. Sansom, Marc Baaden, Christophe Oguey. Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network. Scientific Reports, 2018, 8, pp.13540. ⟨10.1038/s41598-018-31422-5⟩. ⟨hal-01883877⟩
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Jens-Christian M Röper, Démosthène Mitrossilis, Guillaume Stirnemann, François Waharte, Isabel Brito, et al.. The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo. eLife, 2018, 7, ⟨10.7554/eLife.33381⟩. ⟨hal-01935588⟩
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Björn Sommer, Marc Baaden, Michael Krone, Andrew Woods. From Virtual Reality to Immersive Analytics in Bioinformatics. Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180043. ⟨10.1515/jib-2018-0043⟩. ⟨hal-01935682⟩
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Alexandre Maes, Xavier Martinez, Karen Druart, Benoist Laurent, Sean Guégan, et al.. MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180006. ⟨10.1515/jib-2018-0006⟩. ⟨hal-01935585⟩
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Mikael Trellet, Nicolas Ferey, Jakub Flotyński, Marc Baaden, Patrick Bourdot. Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180004. ⟨10.1515/jib-2018-0004⟩. ⟨hal-01935586⟩
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Istvan Kocsis, Mirco Sorci, Heather Vanselous, Samuel Murail, Stephanie Sanders, et al.. Oriented chiral water wires in artificial transmembrane channels. Science Advances , 2018, 4 (3), pp.eaao5603. ⟨10.1126/sciadv.aao5603⟩. ⟨hal-01797309⟩
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Olivier Delalande, Anne-Elisabeth Molza, Raphael dos Santos Morais, Angélique Chéron, Emeline Pollet, et al.. Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions. Journal of Biological Chemistry, 2018, 293 (18), pp.6637-6646. ⟨10.1074/jbc.M117.809798⟩. ⟨hal-01795395v2⟩
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Marc Baaden, Olivier Delalande, Nicolas Ferey, Samuela Pasquali, Jérôme Waldispühl, et al.. Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Computational Biology, 2018, 14 (3), pp.e1005955. ⟨10.1371/journal.pcbi.1005955⟩. ⟨hal-01744190⟩
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Samuel Murail, Tudor Vasiliu, Andrei Neamtu, Mihail Barboiu, Fabio Sterpone, et al.. Water permeation across artificial I-quartet membrane channels: from structure to disorder. Faraday Discussions, 2018, 209, pp.125 - 148. ⟨10.1039/c8fd00046h⟩. ⟨hal-01926847⟩
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Marc Baaden, Mihail Barboiu, Roslyn Bill, Chun-Long Chen, Jeffery Davis, et al.. Biomimetic water channels: general discussion. Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩. ⟨hal-01926861⟩
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Fabio Sterpone, Sébastien Doutreligne, Thanh Thuy Tran, Simone Melchionna, Marc Baaden, et al.. Multi-scale simulations of biological systems using the OPEP coarse-grained model. Biochemical and Biophysical Research Communications, 2018, 498 (2), pp.296-304. ⟨10.1016/j.bbrc.2017.08.165⟩. ⟨hal-01644564⟩
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Vivek Pratap Hitaishi, Romain Clément, Nicolas Bourassin, Marc Baaden, Anne de Poulpiquet, et al.. Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts, 2018, 8 (5), pp.192. ⟨10.3390/catal8050192⟩. ⟨hal-01793660⟩
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Ahmad Elbahnsi, Romain Retureau, Marc Baaden, Brigitte Hartmann, Christophe Oguey. Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution. Journal of Chemical Theory and Computation, 2018, 14 (2), pp.1045 - 1058. ⟨10.1021/acs.jctc.7b00936⟩. ⟨hal-01935581⟩
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Marc Baaden, Mihail Barboiu, Manash Pratim Borthakur, Chun-Long Chen, Rob Coalson, et al.. Applications to water transport systems: general discussion. Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩. ⟨hal-01926896⟩
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Marc Baaden, Mihail Barboiu, Roslyn Bill, Serena Casanova, Chun-Long Chen, et al.. Structure and function of natural proteins for water transport: general discussion. Faraday Discussions, 2018, 209, pp.83 - 95. ⟨10.1039/C8FD90019A⟩. ⟨hal-01926768⟩
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Book sections
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Marc Baaden, Manash Pratim Borthakur, Serena Casanova, Rob Coalson, Viatcheslav Freger, et al.. The modelling and enhancement of water hydrodynamics: general discussion. Faraday Discussions, 209, pp.273-285, 2018, ⟨10.1039/C8FD90021C⟩. ⟨hal-02370038⟩
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2017
Journal articles
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Bogdan Lev, Samuel Murail, Frédéric Poitevin, Brett A Cromer, Marc Baaden, et al.. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (21), pp.E4158 - E4167. ⟨10.1073/pnas.1617567114⟩. ⟨hal-01644525⟩
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Liuba Mazzanti, Sébastien Doutreligne, Cédric Gageat, Philippe Derreumaux, Antoine Taly, et al.. What Can Human-Guided Simulations Bring to RNA Folding?. Biophysical Journal, 2017, 113 (2), pp.302 - 312. ⟨10.1016/j.bpj.2017.05.047⟩. ⟨hal-01644519⟩
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Dario de Vecchis, Laetitia Cavellini, Marc Baaden, Jérôme Hénin, Mickaël M. Cohen, et al.. A membrane-inserted structural model of the yeast mitofusin Fzo1. Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩. ⟨hal-01581980⟩
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Shahid M. Nayeem, Francesco Oteri, Marc Baaden, Shashank Deep. Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3. Journal of Physical Chemistry B, 2017, 121 (22), pp.5483 - 5498. ⟨10.1021/acs.jpcb.7b01867⟩. ⟨hal-01587914⟩
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B. Kozlíková, M. Krone, M. Falk, N. Lindow, Marc Baaden, et al.. Visualization of Biomolecular Structures: State of the Art Revisited. Computer Graphics Forum, 2017, 36 (8), pp.178-204. ⟨10.1111/cgf.13072⟩. ⟨hal-01400465⟩
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Conference papers
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Naif Alharbi, Mohammed Alharbi, Xavier Martinez, Michael Krone, Alexander S. Rose, et al.. Molecular Visualization of Computational Biology Data: A Survey of Surveys. EuroVis 2017 - Short Papers, Jun 2017, Barcelone, Spain. ⟨10.2312/eurovisshort.20171146⟩. ⟨hal-01644549⟩
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2016
Journal articles
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M. Krone, B. Kozlíková, N. Lindow, Marc Baaden, D. Baum, et al.. Visual Analysis of Biomolecular Cavities: State of the Art. Computer Graphics Forum, 2016, 35 (3), pp.527 - 551. ⟨10.1111/cgf.12928⟩. ⟨hal-01400464⟩
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Erol Licsandru, Istvan Kocsis, Yue-Xiao Shen, Samuel Murail, Yves-Marie Legrand, et al.. Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. Journal of the American Chemical Society, 2016, 138 (16), pp.5403 - 5409. ⟨10.1021/jacs.6b01811⟩. ⟨hal-01400466⟩
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Benoist Laurent, Samuel Murail, Azadeh Shahsavar, Ludovic Sauguet, Marc Delarue, et al.. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure, 2016, 24 (4), pp.595 - 605. ⟨10.1016/j.str.2016.02.014⟩. ⟨hal-01400467⟩
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Conference papers
ref_biblio
Mickael Trellet, Nicolas Férey, Marc Baaden, Patrick 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, Mar 2016, Greenville, SC, United States. pp.48-53, ⟨10.1109/IMMERSIVE.2016.7932383⟩. ⟨hal-01497990⟩
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2015
Journal articles
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Maria Vittoria Cubellis, Marc Baaden, Giuseppina Andreotti. Taming molecular flexibility to tackle rare diseases.. Biochimie, 2015, 113, pp.54-8. ⟨10.1016/j.biochi.2015.03.018⟩. ⟨hal-01230761⟩
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Benoist Laurent, Matthieu Chavent, Tristan Cragnolini, Anna Caroline E Dahl, Samuela Pasquali, et al.. Epock : rapid analysis of protein pocket dynamics. Bioinformatics, 2015, 31 (9), pp.1478-1480. ⟨10.1093/bioinformatics/btu822⟩. ⟨hal-01230764⟩
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Serge Pérez, Thibault Tubiana, Anne Imberty, Marc Baaden. Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.. Glycobiology, 2015, 25 (5), pp.483-91. ⟨10.1093/glycob/cwu133⟩. ⟨hal-01230766⟩
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Gustavo Moraga-Cid, Ludovic Sauguet, Christèle Huon, Laurie Malherbe, Christine Girard-Blanc, et al.. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (9), pp.2865-70. ⟨10.1073/pnas.1417864112⟩. ⟨hal-01230762⟩
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Tyler Reddy, David Shorthouse, Daniel L Parton, Elizabeth Jefferys, Philip W Fowler, et al.. Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure, 2015, 23 (3), pp.584-97. ⟨10.1016/j.str.2014.12.019⟩. ⟨hal-01230763⟩
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T. Cragnolini, S. Doutreligne, Marc Baaden, Philippe Derreumaux, S. Pasquali. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure and Dynamics, 2015, 33, pp.30--31. ⟨10.1080/07391102.2015.1032593⟩. ⟨hal-01498028⟩
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Conference papers
ref_biblio
M. Trellet, N. Ferey, Marc Baaden, 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, Mar 2015, Arles, France. pp.31--36, ⟨10.1109/VARMS.2015.7151726⟩. ⟨hal-01498020⟩
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S. Doutreligne, C. Gageat, T. Cragnolini, A. Taly, S. Pasquali, et al.. 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, Mar 2015, Arles, France. pp.1--6, ⟨10.1109/VARMS.2015.7151718⟩. ⟨hal-01498023⟩
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Proceedings
ref_biblio
Barbora Kozlíková, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, et al.. Visualization of Biomolecular Structures: State of the Art. EuroVisSTAR2015, The Eurographics Association, 2015, Eurographics Conference on Visualization (EuroVis) - STARs, ⟨10.2312/eurovisstar.20151112⟩. ⟨hal-03902339⟩
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2014
Journal articles
ref_biblio
Francesco Oteri, Marc Baaden, Elisabeth Lojou, Sophie Sacquin-Mora. Multiscale Simulations Give Insight into the Hydrogen in- and out-Pathways of [NiFe]-Hydrogenases from Aquifex Aeolicus and Desulfovibrio Fructosovorans.. Journal of Physical Chemistry B, 2014, 118 (48), pp.13800-13811. ⟨10.1021/jp5089965⟩. ⟨hal-01084622⟩
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Jonathan D Hirst, David R Glowacki, Marc Baaden. Molecular simulations and visualization: introduction and overview.. Faraday Discussions, 2014, 169, pp.9-22. ⟨10.1039/c4fd90024c⟩. ⟨hal-01084628⟩
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Fabio Sterpone, Simone Melchionna, Pierre Tuffery, Samuela Pasquali, Normand Mousseau, et al.. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.. Chemical Society Reviews, 2014, pp.4871-93. ⟨10.1039/C4CS00048J⟩. ⟨hal-01084631⟩
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A. Tek, Marc Baaden, N. Férey, P. Bourdot. MANHaptic: A Haptic Adaptive Method for Precise Manipulation, Assembly and Navigation. International Journal on Human Machine Interaction, 2014, 1, pp.57-63. ⟨hal-01498081⟩
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Francesco Oteri, Alexandre Ciaccafava, Anne De Poulpiquet, Marc Baaden, Elisabeth. Lojou, et al.. The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Physical Chemistry Chemical Physics, 2014, 16 (23), pp.11318-11322. ⟨10.1039/C4CP00510D⟩. ⟨hal-01493492⟩
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Matthieu Dreher, Jessica Prevoteau-Jonquet, Mikael Trellet, Marc Piuzzi, Marc Baaden, et al.. ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations. Faraday Discussions, 2014, Molecular simulations and visualization, 169, pp.119-142. ⟨10.1039/C3FD00142C⟩. ⟨hal-00942627⟩
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Mian Wang, Marc Baaden, Jianyi Wang, Zhiqun Liang. A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450.. Journal of Chemical Information and Modeling, 2014, pp.1218-25. ⟨10.1021/ci400660e⟩. ⟨hal-01084632⟩
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Anne-Elisabeth Molza, Nicolas Férey, Mirjam Czjzek, Elisabeth Le Rumeur, Jean-François Hubert, et al.. Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discussions, 2014, 169, pp.45-62. ⟨10.1039/C3FD00134B⟩. ⟨hal-01018071⟩
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Fabio Sterpone, Simone Melchionna, Pierre Tuffery, Samuela Pasquali, Normand Mousseau, et al.. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chemical Society Reviews, 2014, 43 (13), pp.4871-4893. ⟨10.1039/c4cs00048j⟩. ⟨hal-04193590⟩
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Conference papers
ref_biblio
S. Doutreligne, T. Cragnolini, S. Pasquali, P. Derreumaux, Marc Baaden. UnityMol: Interactive scientific visualization for integrative biology. IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV) 2014, 2014, Paris, France. pp.109--110. ⟨hal-01498055⟩
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ref_biblio
M. Trellet, Nicolas 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, 2014, Angers, France. pp.76--81, ⟨10.5220/0004914300760081⟩. ⟨hal-01498053⟩
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Book sections
ref_biblio
Jérôme Hénin, Marc Baaden, Antoine 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, pp.347--392, 2014, 978-1-4939-0661-1. ⟨10.1007/978-1-4939-0662-8_13⟩. ⟨hal-01498051⟩
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Other publications
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Marc Baaden, Matthieu Dreher, Nicolas Ferey, Sébastien Limet, Jessica Prevoteau-Jonquet, et al.. Vitamins : Visual and In Situ Analytics for Molecular Interactive Simulation. 2014. ⟨hal-01313096⟩
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2013
Journal articles
ref_biblio
Marc Baaden, Siewert J Marrink. Coarse-grain modelling of protein-protein interactions.. Current Opinion in Structural Biology, 2013, 23 (6), pp.878-86. ⟨10.1016/j.sbi.2013.09.004⟩. ⟨hal-01084639⟩
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Daniel L Parton, Alex Tek, Marc Baaden, Mark S P Sansom. Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations.. PLoS Computational Biology, 2013, 9 (4), pp.e1003034. ⟨10.1371/journal.pcbi.1003034⟩. ⟨hal-01084643⟩
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Ludovic Sauguet, Frédéric Poitevin, Samuel Murail, Catherine van Renterghem, Gustavo Moraga-Cid, et al.. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.. EMBO Journal, 2013, 32 (5), pp.728-41. ⟨10.1038/emboj.2013.17⟩. ⟨hal-01084646⟩
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Zhihan Lv, Alex Tek, Franck da Silva, Charly Empereur-Mot, Matthieu Chavent, et al.. Game on, science - how video game technology may help biologists tackle visualization challenges.. PLoS ONE, 2013, 8 (3), pp.e57990. ⟨10.1371/journal.pone.0057990⟩. ⟨hal-01084644⟩
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Dominique Costa, Pierre-Alain Garrain, Marc Baaden. Understanding small biomolecule-biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces.. Journal of Biomedical Materials Research Part A, 2013, 101A (4), pp.1210-1222. ⟨10.1002/jbm.a.34416⟩. ⟨hal-00760127⟩
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Marc Baaden, Marc Delarue. Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallography. ESRF Highlights, 2013, pp.44-45. ⟨hal-01498088⟩
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Matthieu Dreher, Marc Piuzzi, Ahmed Turki, Matthieu Chavent, Marc Baaden, et al.. Interactive Molecular Dynamics: Scaling up to Large Systems. Procedia Computer Science, 2013, 2013 International Conference on Computational Science, 18, pp.20-29. ⟨10.1016/j.procs.2013.05.165⟩. ⟨hal-01084652⟩
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Conference papers
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Matthieu Dreher, Marc Piuzzi, Turki Ahmed, Chavent Matthieu, Marc Baaden, et al.. Interactive Molecular Dynamics: Scaling up to Large Systems. International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain. ⟨hal-00809024⟩
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Francesco Oteri, Anne de Poulpiquet, Alexandre Ciaccafava, Elisabeth Lojou, Marc Baaden. Molecular Modeling of Hydrogenase Enzymes for Biofuel Cell Design. 57th Annual Meeting of the Biophysical-Society, Feb 2013, Philadelphia, United States. pp.335a, ⟨10.1016/j.bpj.2012.11.1864⟩. ⟨hal-03079239⟩
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M. Trellet, N. Férey, M. Baaden, P. Bourdot. Navigation guidée par le contenu pour l'exploration moléculaire.. Journées de l’Association Française de Réalité Virtuelle (AFRV), 2013, Laval, France. ⟨hal-01498083⟩
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Proceedings
ref_biblio
Benoist Laurent, Samuel Murail, Franck da Silva, Pierre-Jean Corringer, Marc Baaden. Modeling complex biological systems: From solution chemistry to membranes and channels. Pure and Applied Chemistry, 85 (1), pp.1-13, 2013, ⟨10.1351/PAC-CON-12-04-10⟩. ⟨hal-00760163⟩
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2012
Journal articles
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Leonardo Darré, Alex Tek, Marc Baaden, Sergio Pantano. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. Journal of Chemical Theory and Computation, 2012, 8 (10), pp.3880-3894. ⟨10.1021/ct3001816⟩. ⟨hal-00760151⟩
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Marie S Prevost, Ludovic Sauguet, Hugues Nury, Catherine van Renterghem, Christèle Huon, et al.. A locally closed conformation of a bacterial pentameric proton-gated ion channel.. Nature Structural and Molecular Biology, 2012, 19 (6), pp.642-9. ⟨10.1038/nsmb.2307⟩. ⟨hal-00760125⟩
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Matthieu Chavent, Marc Baaden, Éric Hénon, Serge 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. L'Actualité Chimique, 2012, 363, pp.42-46. ⟨hal-00760143⟩
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Conference papers
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Nicolas Ferey, Olivier Delalande, Marc Baaden. BioSpring: an interactive and multi-resolution software for flexible docking and for mechanical exploration of large biomolecular assemblies. JOBIM 2012 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.433-434. ⟨hal-00761683⟩
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Book sections
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Alex Tek, Benoist Laurent, Marc Piuzzi, Zhihan Lu, Matthieu Chavent, et al.. Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations. Weibo Cai and Hao Hong. Biochemistry, Genetics and Molecular Biology " "Protein-Protein Interactions - Computational and Experimental Tools", InTech, pp.27-65, 2012, 978-953-51-0397-4. ⟨10.5772/36568⟩. ⟨hal-00760181⟩
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Other publications
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Marc Baaden. Visualiser, toucher, déformer et assembler des nano-objets du bout des doigts. Les nanotechnologies : un nouveau paradigme, Les Cahiers de l’ANR - n°5, 2012, pp.47. ⟨hal-03948139v2⟩
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2011
Journal articles
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Matthieu Chavent, Bruno Lévy, Michael Krone, Katrin Bidmon, Jean-Philippe Nominé, et al.. GPU-powered tools boost molecular visualization.. Briefings in Bioinformatics, 2011, 12 (6), pp.689-701. ⟨10.1093/bib/bbq089⟩. ⟨hal-00645161⟩
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Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, et al.. GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.. Journal of Computational Chemistry, 2011, 32 (13), pp.2924-35. ⟨10.1002/jcc.21861⟩. ⟨hal-00645162⟩
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Olivier Delalande, Sophie Sacquin-Mora, Marc Baaden. Enzyme closure and nucleotide binding structurally lock guanylate kinase.. Biophysical Journal, 2011, 101 (6), pp.1440-9. ⟨10.1016/j.bpj.2011.07.048⟩. ⟨hal-00645163⟩
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Laurent J Catoire, Marjorie Damian, Marc Baaden, Eric Guittet, Jean-Louis Banères. Electrostatically-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 range.. Journal of Biomolecular NMR, 2011, 50 (3), pp.191-195. ⟨10.1007/s10858-011-9523-3⟩. ⟨hal-03011659⟩
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Hugues Nury, Catherine van Renterghem, Yun Weng, Alphonso Tran, Marc Baaden, et al.. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel.. Nature, 2011, 469 (7330), pp.428-31. ⟨10.1038/nature09647⟩. ⟨hal-00645160⟩
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Conference papers
ref_biblio
Marc Baaden. Illustration moléculaire en Chimie et Biologie : exemples, état de l’art et perspectives. Du réel à l'image, Congrès de l’AEIMS, Nov 2011, Strasbourg, France. pp.74-78. ⟨hal-03948334⟩
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Marc Baaden. Molecular Illustration in Chemistry and Biology: examples, state-of-art and outlook. Reality Through Image, AEIMS Congress, Nov 2011, Strasbourg, France. pp.74-78. ⟨hal-03948350⟩
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Matthieu Chavent, Marc Piuzzi, Alex Tek, Marc Baaden. FvNano: A Virtual Laboratory to Manipulate Molecular Systems. 1st IEEE symposium on biological data visualization, @ ieee visweek, 2011, Oct 2011, Providence, RI, United States. pp.136. ⟨hal-01498124⟩
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Proceedings
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Marc Baaden. La réalité virtuelle au laboratoire de Biochimie Théorique - toucher, déformer et assembler des molécules du bout des doigts. Journal de l'AFRV, 10, pp.4-5, 2011. ⟨hal-03948409⟩
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2010
Journal articles
ref_biblio
Sophie Sacquin-Mora, Olivier Delalande, Marc Baaden. Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress. Biophysical Journal, 2010, 99 (10), pp.3412-3419. ⟨10.1016/j.bpj.2010.09.026⟩. ⟨hal-00602505⟩
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Yubo Zhang, Marc Baaden, Junjie Yan, Jinzhen Shao, Su Qiu, et al.. The Molecular Recognition Mechanism for Superoxide Dismutase Presequence Binding to the Mitochondrial Protein Import Receptor Tom20 from Oryza sativa Involves an LRTLA Motif. Journal of Physical Chemistry B, 2010, 114 (43), pp.13839-13846. ⟨10.1021/jp103547s⟩. ⟨hal-03904752⟩
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Adrien Saladin, Christopher Amourda, Pierre Poulain, Nicolas Férey, Marc Baaden, et al.. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.. Nucleic Acids Research, 2010, 38 (19), pp.6313-23. ⟨10.1093/nar/gkq459⟩. ⟨hal-00533099⟩
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Hugues Nury, Frédéric Poitevin, Catherine van Renterghem, Jean-Pierre Changeux, Pierre-Jean Corringer, et al.. One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (14), pp.6275-6280. ⟨10.1073/pnas.1001832107⟩. ⟨pasteur-02174737⟩
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Deepak Kumar Sinha, Pierre Neveu, Nathalie Gagey, Isabelle Aujard, Chouaha Benbrahim-Bouzidi, et al.. Photocontrol of Protein Activity in Cultured Cells and Zebrafish with One- and Two-Photon Illumination. ChemBioChem, 2010, 11 (5), pp.653-663. ⟨10.1002/cbic.201000008⟩. ⟨hal-03904748⟩
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Pierre-Jean Corringer, Marc Baaden, Nicolas Bocquet, Marc Delarue, Virginie Dufresne, et al.. Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. The Journal of Physiology, 2010, 588 (4), pp.565-572. ⟨10.1113/jphysiol.2009.183160⟩. ⟨pasteur-02174745⟩
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Marc Guéroult, Daniel Picot, Joséphine Abi-Ghanem, Brigitte Hartmann, Marc Baaden. How cations can assist DNase I in DNA binding and hydrolysis.. PLoS Computational Biology, 2010, 6 (11), pp.e1001000. ⟨10.1371/journal.pcbi.1001000⟩. ⟨hal-00645165⟩
Olivier Delalande, Nicolas Ferey, Benoist Laurent, Marc Gueroult, Brigitte Hartmann, et al.. Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.. Pacific Symposium on Biocomputing, 2010, pp.205-15. ⟨10.1142/9789814295291_0023⟩. ⟨hal-00661430⟩
Matthieu Chavent, Antoine Vanel, Alex Teck, Bruno Levy, Bruno Raffin, et al.. A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), 2010, Unknown, France. ⟨hal-00953423⟩
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Book sections
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Philippe Hapiot, Mustapha Abdelmoula, Xavier Assfeld, Jean Aupiais, Marc Baaden, et al.. Physicochimie : molécules, milieux. RAPPORT DE CONJONCTURE 2010 du Comité national de la recherche scientifique, CNRS Editions, pp.243-263, 2010, 978-2-271-07263-4. ⟨hal-03977638⟩
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Syma Khalid, Marc Baaden. Chapter 9. Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels. Molecular Simulations and Biomembranes, Royal Society of Chemistry, pp.225-247, 2010, RSC Biomolecular Sciences, ⟨10.1039/9781849732154-00225⟩. ⟨hal-03904759⟩
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Habilitation à diriger des recherches
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Marc Baaden. Simulations numériques de systèmes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes. Sciences pharmaceutiques. Université Paris-Diderot - Paris VII, 2010. ⟨tel-00541521⟩
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Other publications
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Marc Baaden. Toucher, déformer et assembler des molécules du bout des doigts. Le calcul intensif: technologie clé pour le futur, Les Cahiers de l'ANR - n° 3, 2010, pp.71. ⟨hal-03977530⟩
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Poster communications
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Alex Tek, Benoist Laurent, Nicolas Férey, Marc Baaden. A Multimodal VR Framework for Interactive Molecular Simulations. EuroVR-EVE 2010, Nov 2010, Orsay, France. ⟨hal-03977463⟩
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2009
Journal articles
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Olivier Delalande, Nicolas Férey, Gilles Grasseau, Marc Baaden. Complex molecular assemblies at hand via interactive simulations.. Journal of Computational Chemistry, 2009, 30 (15), pp.2375-87. ⟨10.1002/jcc.21235⟩. ⟨inserm-00713313⟩
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Marie-Pierre Durrieu, Peter Bond, Mark Sansom, Richard Lavery, Marc Baaden. Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States. ChemPhysChem, 2009, 10 (9-10), pp.1548-1552. ⟨10.1002/cphc.200900216⟩. ⟨hal-03904871⟩
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Nicolas Bocquet, Hugues Nury, Marc Baaden, Chantal Le Poupon, Jean-Pierre Changeux, et al.. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature, 2009, 457 (7225), pp.111-114. ⟨10.1038/nature07462⟩. ⟨pasteur-02175132⟩
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Books
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Axel Kahn, Sebastien Fleuret, Sébastien Descotes-Genon, Nicolas B. Garnier, Carole Levenes, et al. (Dir.). Itinéraires Bis. 2009, Connaissance et savoirs, 978-2-7539-0164-3. ⟨halshs-02424173⟩
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2008
Journal articles
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Katherine Cox, Peter Bond, Alessandro Grottesi, Marc Baaden, Mark Sansom. Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. European Biophysics Journal, 2008, 37 (2), pp.131-141. ⟨10.1007/s00249-007-0185-8⟩. ⟨hal-03904877⟩
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Marilisa Neri, Marc Baaden, Vincenzo Carnevale, Claudio Anselmi, Amos Maritan, et al.. Microseconds Dynamics Simulations of the Outer-Membrane Protease T. Biophysical Journal, 2008, 94 (1), pp.71-78. ⟨10.1529/biophysj.107.116301⟩. ⟨hal-03904879⟩
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Mp Durrieu, R. Lavery, Marc Baaden. Interactions between neuronal fusion proteins explored by molecular dynamics.. Biophysical Journal, 2008, 94 (9), pp.3436-3446. ⟨10.1529/biophysj.107.123117⟩. ⟨hal-00315180⟩
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Conference papers
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Nicolas Férey, Olivier Delalande, Gilles Grasseau, Marc Baaden. A VR framework for interacting with molecular simulations. the 2008 ACM symposium, Oct 2008, Bordeaux, France. pp.91-94, ⟨10.1145/1450579.1450598⟩. ⟨hal-03904892⟩
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Nicolas Férey, Olivier Delalande, Gilles Grasseau, Marc Baaden. From Interactive to Immersive Molecular Dynamics. Workshop in Virtual Reality Interactions and Physical Simulation "VRIPHYS" (2008), 2008, Grenoble, France. pp.89-96, ⟨10.2312/PE/vriphys/vriphys08/089-096⟩. ⟨hal-03904907⟩
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2007
Journal articles
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Kaihsu Tai, Marc Baaden, Stuart Murdock, Bing Wu, Muan Hong Ng, et al.. Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database. Journal of Molecular Graphics and Modelling, 2007, 25 (6), pp.896-902. ⟨10.1016/j.jmgm.2006.08.010⟩. ⟨hal-03905209⟩
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Conference papers
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Elmar Krieger, Laurent Leger, Marie-Pierre Durrieu, Nada Taib, Peter Bond, et al.. Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex: a Grand Challenge Project on the DEISA HPC Infrastructure. Parallel Computing: Architectures, Algorithms and Applications, Sep 2007, Julich, Germany. pp.729-736. ⟨hal-03907311⟩
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Book sections
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Marc Baaden, Richard Lavery. There's plenty of room in the middle: Multiscale Modelling of Biological Systems. Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Singpost, pp.173-196, 2007, 978-81-309-0208-4. ⟨hal-03907310⟩
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2005
Journal articles
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Richard Law, Charlotte Capener, Marc Baaden, Peter Bond, Jeff Campbell, et al.. Membrane protein structure quality in molecular dynamics simulation. Journal of Molecular Graphics and Modelling, 2005, 24 (2), pp.157-165. ⟨10.1016/j.jmgm.2005.05.006⟩. ⟨hal-03907341⟩
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2004
Journal articles
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José Faraldo-Gómez, Lucy Forrest, Marc Baaden, Peter Bond, Carmen Domene, et al.. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins - Structure, Function and Bioinformatics, 2004, 57 (4), pp.783-791. ⟨10.1002/prot.20257⟩. ⟨hal-03907343⟩
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Marc Baaden, Mark S.P. Sansom. OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme. Biophysical Journal, 2004, 87 (5), pp.2942-2953. ⟨10.1529/biophysj.104.046987⟩. ⟨hal-03907344⟩
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2003
Journal articles
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Marc Baaden, Christoph Meier, Mark Sansom, Mark S.P. Sansom. A Molecular Dynamics Investigation of Mono and Dimeric States of the Outer Membrane Enzyme OMPLA. Journal of Molecular Biology, 2003, 331 (1), pp.177-189. ⟨10.1016/s0022-2836(03)00718-6⟩. ⟨hal-03911449⟩
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Jeff Campbell, Philip Biggin, Marc Baaden, Mark Sansom. Extending the Structure of an ABC Transporter to Atomic Resolution: Modeling and Simulation Studies of MsbA. Biochemistry, 2003, 42 (13), pp.3666-3673. ⟨10.1021/bi027337t⟩. ⟨hal-03911326⟩
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Marc Baaden, Frédéric Berny, Charles Madic, Rachel Schurhammer, Georges Wipff. Theoretical Studies on Lanthanide Cation Extraction by Picolinamides: Ligand–Cation Interactions and Interfacial Behavior. Solvent Extraction and Ion Exchange, 2003, 21 (2), pp.199-220. ⟨10.1081/SEI-120018946⟩. ⟨hal-02951773⟩
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Theses
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Marc Baaden. Etudes de molécules extractantes en solution et aux interfaces liquide-liquide : aspects structuraux et mécanistiques des effets de synergie. Autre. Université Louis Pasteur - Strasbourg I, 2003. Français. ⟨NNT : ⟩. ⟨tel-00002812v2⟩
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2002
Journal articles
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Marc Baaden, Rachel Schurhammer, Georges Wipff. 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, 2002, 106 (2), pp.434-441. ⟨10.1021/jp0123785⟩. ⟨hal-03165795⟩
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2001
Journal articles
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Marc Baaden, M. Burgard, G. Wipff. TBP at the Water−Oil Interface: The Effect of TBP Concentration and Water Acidity Investigated by Molecular Dynamics Simulations. Journal of Physical Chemistry B, 2001, 105 (45), pp.11131-11141. ⟨10.1021/jp011890n⟩. ⟨hal-03911461⟩
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Marc Baaden, Michel Burgard, Christian Boehme, Georges Wipff. 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, 2001, 3 (7), pp.1317-1325. ⟨10.1039/B009859K⟩. ⟨hal-03911468⟩
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Marc Baaden, F. Berny, G. Wipff. The chloroform / TBP / aqueous nitric acid interfacial system: a molecular dynamics investigation. Journal of Molecular Liquids, 2001, 90 (1-3), pp.1-9. ⟨10.1016/S0167-7322(00)00174-4⟩. ⟨hal-03911463⟩
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2000
Journal articles
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Marc Baaden, F. Berny, C. Madic, G. Wipff. M 3+ 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, 2000, 104 (32), pp.7659-7671. ⟨10.1021/jp001352v⟩. ⟨hal-03920006⟩
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Marc Baaden, Georges Wipff, Mohamed Reza Yaftian, Michel Burgard, Dominique Matt. 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, 2000, 7, pp.1315-1322. ⟨10.1039/B000019L⟩. ⟨hal-03920024⟩
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Bernard Lambert, Vincent Jacques, Alexander Shivanyuk, Susan Matthews, Abdi Tunayar, et al.. Calix[4]arenes as Selective Extracting Agents. An NMR Dynamic and Conformational Investigation of the Lanthanide(III) and Thorium(IV) Complexes. Inorganic Chemistry, 2000, 39 (10), pp.2033-2041. ⟨10.1021/ic990683n⟩. ⟨hal-03920094⟩
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Marc Baaden, P. Granger, A. Strich. 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 H 2 C=CH-X. Molecular Physics, 2000, 98 (6), pp.329-342. ⟨10.1080/00268970009483297⟩. ⟨hal-03920108⟩
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L. Troxler, Marc Baaden, V. Böhmer, G. Wipff. Complexation of M 3+ Lanthanide Cations by Calix[4]arene-CMPO Ligands: A Molecular Dynamics Study in Methanol Solution and at a Water/Chloroform Interface. Supramolecular Chemistry, 2000, 12 (1), pp.27-51. ⟨10.1080/10610270008029803⟩. ⟨hal-03919995⟩
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Marc Baaden, Frédéric Berny, Christian Boehme, Nicolas Muzet, Rachel Schurhammer, et al.. Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study. Journal of Alloys and Compounds, 2000, 303, pp.104-111. ⟨10.1016/S0925-8388(00)00657-5⟩. ⟨hal-02956544⟩
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Book sections
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Marc Baaden, F. Berny, N. Muzet, L. Troxler, G. Wipff. Interfacial Features of Assisted Liquid-Liquid Extraction of Uranyl and Cesium Salts: A Molecular Dynamics Investigation. Calixarenes for Separations, 757, American Chemical Society, pp.71-85, 2000, ACS Symposium Series, ⟨10.1021/bk-2000-0757.ch006⟩. ⟨hal-03920161⟩
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Other publications
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Marc Baaden. Molecular Modeling with the ChemOffice Ultra 4.5 Program Suite. 2000. ⟨hal-03921142⟩
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1999
Conference papers
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Marc Baaden, F. Berny, N. Muzet, R. Schurhammer, Laurent Troxler, et al.. Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores. Euradwaste 1999: radioactive Waste Management Strategies and Issues, Fifth European Commission Conference on Radioactive Waste Management and Disposal and Decommissioning, Nov 1999, Luxembourg, Luxembourg. pp.390-393. ⟨hal-03920295⟩
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