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Hire Dr. Marc B.
France
USD 180 /hr
Computational chemistry innovator, VR enthusiast, and mindful science consultant: molecules, tech, and life optimization
Profile Summary
Subject Matter Expertise
Services
Writing
Technical Writing,
Copywriting,
Creative Writing
Research
Fact Checking,
Scientific and Technical Research
Consulting
Scientific and Technical Consulting
Data & AI
Data Visualization
Work Experience
Research Director
Centre National de la Recherche Scientifique
January 2003 - Present
lecturer
Université Paris Cité
January 2003 - Present
EC Research fellow
University of Oxford
January 2001 - December 2002
Education
Ph.D., Chemistry
Université Louis Pasteur (Strasbourg I) - France
September 1997 - September 2000
Certifications
- Certification details not provided.
Publications
JOURNAL ARTICLE
Marc Baaden, Bogdan Lev, Samuel Murail, Igor Vorobyov, Toby W. Allen (2025). State-Dependent Dynamic Communication Networks in a Pentameric Ligand-Gated Ion Channel . The Journal of Physical Chemistry B.
Marc Baaden, Diego Barquero Morera, Giovanni Mattiotti, Alexandar Kocev, Amshuman Rousselot, Louis Meuret, Lucas Rouaud, Hubert Santuz, Antoine Taly, Samuela Pasquali (2025). Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets . Journal of Chemical Theory and Computation.
Marc Baaden, Baptiste Etcheverry, Aurélien de la Lande, Fabien Cailliez (2025). NOX Transmembrane Electron Transfer Is Governed by a Subtly Balanced, Self-Adjusting Charge Distribution . Journal of Chemical Information and Modeling.
Marc Baaden, David R. Glowacki (2025). Virtual reality in drug design: Benefits, applications and industrial perspectives . Current Opinion in Structural Biology.
Marc Baaden, Benoist Laurent, André Lanrezac, Hubert Santuz, Nicolas Ferey, Olivier Delalande (2025). BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics . Protein Science.
Marc Baaden, Li-Bo Huang, Dan-Dan Su, Arthur Hardiagon, Istvan Kocsis, Arie van der Lee, Fabio Sterpone, Mihail Barboiu (2025). Water-Pore Flow Permeation through Multivalent H-Bonding Pyridine-2,6-dicarboxamide-histamine/Histidine Water Channels . Journal of the American Chemical Society.
Marc Baaden (2024). MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform . The Journal of Physical Chemistry B.
Marc Baaden, Johanna KS Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J Howard, Lucie Delemotte, Erik Lindahl, Kresten Lindorff-Larsen, et al. (2024). MDverse, shedding light on the dark matter of molecular dynamics simulations . eLife.
Marc Baaden, Johanna KS Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J Howard, Lucie Delemotte, Erik Lindahl, Kresten Lindorff-Larsen, et al. (2024). MDverse, shedding light on the dark matter of molecular dynamics simulations . eLife.
Marc Baaden, Raphaelle Versini, Sujith Sritharan, Burcu Aykac Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, et al. (2024). A Perspective on the Prospective Use of AI in Protein Structure Prediction . Journal of Chemical Information and Modeling.
Marc Baaden, Iuliana M. Andrei, Wenzhang Chen, Stéphane P. Vincent, Mihail Barboiu (2023). Proton- versus Cation-Selective Transport of Saccharide Rim-Appended Pillar[5]arene Artificial Water Channels . Journal of the American Chemical Society.
Marc Baaden, David Kuťák, Pere‐Pau Vázquez, Tobias Isenberg, Michael Krone, Jan Byška, Barbora Kozlíková, Haichao Miao (2023). State of the Art of Molecular Visualization in Immersive Virtual Environments . Computer Graphics Forum.
Marc Baaden, Li-Bo Huang, Fumihiko Mamiya, Eiji Yashima, Mihail Barboiu (2023). Self-Assembling Peptide-Appended Metallomacrocycle Pores for Selective Water Translocation . ACS Applied Materials & Interfaces.
Marc Baaden, André Lanrezac (2023). UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape . Membranes.
Marc Baaden, Yubo Zhang (2023). Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT . Catalysts.
Marc Baaden, Yubo Zhang (2023). Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT . Catalysts.
Marc Baaden, André Lanrezac, Benoist Laurent, Hubert Santuz, Nicolas Férey (2022). Fast and Interactive Positioning of Proteins within Membranes . Algorithms.
Artificial Water Channels Form Precursors to Sponge-Like Aggregates in Water–Ethanol Mixtures <head>
<META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent">
</head> . The Journal of Physical Chemistry A.
Marc Baaden, Davide Spalvieri, Anne-Marine Mauviel, Matthieu Lambert, Nicolas Férey, Sophie Sacquin-Mora, Matthieu Chavent (2022). Design – a new way to look at old molecules . Journal of Integrative Bioinformatics.
Marc Baaden, Björn Sommer, Daisuke Inoue (2022). Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design . Journal of Integrative Bioinformatics.
Deep inside molecules - digital twins at the nanoscale <head>
<META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent">
</head> . Virtual Reality & Intelligent Hardware.
Marc Baaden, André Lanrezac, Nicolas Férey (2022). Wielding the power of interactive molecular simulations . WIREs Computational Molecular Science.
Marc Baaden, Staëlle Makamte, Aurélien Thureau, Amira Jabrani, Annick Paquelin, Anne Plessis, Matthieu Sanial, Olga Rudenko, Francesco Oteri, Valérie Biou, et al.(2022). 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. 214. (2). p. 107853. Elsevier {BV}
Marc Baaden, Anne-Elisabeth Molza, Yvonne Westermaier, Magali Moutte, Pierre Ducrot, Claudia Danilowicz, Veronica Godoy-Carter, Mara Prentiss, Charles H. Robert, Chantal Prévost, et al.(2022). Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies . Frontiers in Molecular Biosciences. 9. Frontiers Media {SA}
Marc Baaden, Nicolas Bourassin, Florent Barbault, Sophie Sacquin-Mora(2022). Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces . Langmuir. 38. (4). p. 1313--1323. American Chemical Society ({ACS})
Marc Baaden, Núria López, Luigi Del Debbio, Matej Praprotnik, Laura Grigori, Catarina Simões, Serge Bogaerts, Florian Berberich, Thomas Lippert, Janne Ignatius, et al.(2021). Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic . Proceedings of the National Academy of Sciences. 118. (46). Proceedings of the National Academy of Sciences
Marc Baaden(2021). The never-ending quest to understand the shapes and motions of molecules . The Biochemist. 43. (5). p. 22--24. Portland Press Ltd.
Marc Baaden, Xavier Martinez(2021). 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. 77. (6). p. 746--754. International Union of Crystallography ({IUCr})
Marc Baaden, Arthur Hardiagon, Samuel Murail, Li-Bo Huang, Arie van der Lee, Fabio Sterpone, Mihail Barboiu (2021). Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs . The Journal of Chemical Physics.
Marc Baaden, Xiaojing Wu, Jérôme Hénin, Laura Baciou, Fabien Cailliez, Aurélien de la Lande(2021). Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations . Frontiers in Chemistry. 9. Frontiers Media {SA}
Marc Baaden, Li-Bo Huang, Arthur Hardiagon, Istvan Kocsis, Cristina-Alexandra Jegu, Mihai Deleanu, Arnaud Gilles, Arie van der Lee, Fabio Sterpone, Mihail Barboiu(2021). Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation . Journal of the American Chemical Society. 143. (11). p. 4224--4233. American Chemical Society ({ACS})
Marc Baaden, Dmytro Strilets, Shixin Fa, Arthur Hardiagon, Tomoki Ogoshi, Mihail Barboiu(2020). Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers . Angewandte Chemie International Edition. 59. (51). p. 23213--23219. Wiley
Marc Baaden, Dmytro Strilets, Shixin Fa, Arthur Hardiagon, Tomoki Ogoshi, Mihail Barboiu(2020). Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers . Angewandte Chemie. 132. (51). p. 23413--23419. Wiley
Marc Baaden, Dmytro Strilets, Shixin Fa, Arthur Hardiagon, Tomoki Ogoshi, Mihail Barboiu(2020). Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers . Angewandte Chemie. 132. (51). p. 23413--23419. Wiley
Marc Baaden, Nicolas Bourassin, Elisabeth Lojou, Sophie Sacquin-Mora(2020). Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation . The Journal of Physical Chemistry B. 124. (39). p. 8516--8523. American Chemical Society ({ACS})
Marc Baaden, Xavier Martinez, Matthieu Chavent(2020). Visualizing protein structures — tools and trends . Biochemical Society Transactions. 48. (2). p. 499--506. Portland Press Ltd.
Marc Baaden, Mattia Migliore, Andrea Bonvicini, Vincent Tognetti, Laure Guilhaudis, Hassan Oulyadi, Laurent Joubert, Isabelle Ségalas-Milazzo(2020). 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. 22. (3). p. 1611--1623. Royal Society of Chemistry ({RSC})
Marc Baaden, Mirko Zaffagnini, Christophe H. Marchand, Marco Malferrari, Samuel Murail, Sara Bonacchi, Damiano Genovese, Marco Montalti, Giovanni Venturoli, Giuseppe Falini, et al.(2019). Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates . Proceedings of the National Academy of Sciences. 116. (51). p. 26057--26065. Proceedings of the National Academy of Sciences
Marc Baaden, Joseph A. Laureanti, Juan Brandi, Elvis Offor, David Engel, Robert Rallo, Bojana Ginovska, Xavier Martinez, Nathan A. Baker(2019). Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS . Protein Science. Wiley
Marc Baaden, Astrid F. Brandner, Stepan Timr, Simone Melchionna, Philippe Derreumaux, Fabio Sterpone (2019). Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics . Scientific Reports.
Marc Baaden, Xavier Martinez, Michael Krone, Naif Alharbi, Alexander S. Rose, Robert S. Laramee, Sean O'Donoghue, Matthieu Chavent(2019). Molecular Graphics: Bridging Structural Biologists and Computer Scientists . Structure. 27. (11). p. 1617--1623. Elsevier {BV}
Marc Baaden, Astrid Brandner, Dario De Vecchis, Mickael M. Cohen, Antoine Taly(2019). Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking . Mitochondrion. 49. p. 234--244. Elsevier {BV}
Marc Baaden, Dario De Vecchis, Astrid Brandner, Mickael M. Cohen, Antoine Taly(2019). A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin . The Journal of Membrane Biology. 252. (4-5). p. 293--306. Springer Science and Business Media {LLC}
Marc Baaden, Astrid Brandner, Dario De Vecchis, Mickael M. Cohen, Antoine Taly(2019). Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking . Data in Brief. 26. p. 104460. Elsevier {BV}
A. Taly, F. Nitti, M. Baaden, S. Pasquali(2019). Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching . Interface Focus. 9. (3). p. 20180065. The Royal Society
Marc Baaden(2019). Visualizing Biological Membrane Organization and Dynamics . Journal of Molecular Biology. 431. (10). p. 1889--1919. Elsevier {BV}
Marc Baaden, Mihail Barboiu, Manish Kumar, Philip A. Gale, Bruce J. Hinds(2019). Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK . Chemical Communications. 55. (27). p. 3853--3858. Royal Society of Chemistry ({RSC})
Marc Baaden, Xavier Martinez, Michael Krone(2019). QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces . Workshop on Molecular Graphics and Visual Analysis of Molecular Data. The Eurographics Association
Marc Baaden, Jérémy Esque, Mark S. P. Sansom, Christophe Oguey (2018). Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network . Scientific Reports.
Marc Baaden, Jens-Christian Röper, Démosthène Mitrossilis, Guillaume Stirnemann, François Waharte, Isabel Brito, Maria-Elena Fernandez-Sanchez, Jean Salamero, Emmanuel Farge(2018). The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo . eLife. 7. {eLife} Sciences Organisation, Ltd.
Marc Baaden, Mikael Trellet, Nicolas Férey, Jakub Flotyński, Patrick Bourdot(2018). Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data . Journal of Integrative Bioinformatics. 15. (2). Walter de Gruyter {GmbH}
Marc Baaden, Björn Sommer, Michael Krone, Andrew Woods(2018). From Virtual Reality to Immersive Analytics in Bioinformatics . Journal of Integrative Bioinformatics. 15. (2). Walter de Gruyter {GmbH}
Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M(2018). MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis . Journal of integrative bioinformatics.
Marc Baaden, Vivek Hitaishi, Romain Clement, Nicolas Bourassin, Anne De Poulpiquet, Sophie Sacquin-Mora, Alexandre Ciaccafava, Elisabeth Lojou(2018). Controlling Redox Enzyme Orientation at Planar Electrodes . Catalysts. 8. (5). p. 192. {MDPI} {AG}
(2018). Controlling Redox Enzyme Orientation at Planar Electrodes . Catalysts.
Marc Baaden, Olivier Delalande, Anne-Elisabeth Molza, Raphael Dos Santos Morais, Angélique Chéron, Émeline Pollet, Céline Raguenes-Nicol, Christophe Tascon, Emmanuel Giudice, Marine Guilbaud, et al.(2018). Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions . Journal of Biological Chemistry. 293. (18). p. 6637--6646. Elsevier {BV}
Marc Baaden, Scott Markel, Olivier Delalande, Nicolas Ferey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly (2018). Ten simple rules to create a serious game, illustrated with examples from structural biology . PLOS Computational Biology.
Marc Baaden, Istvan Kocsis, Mirco Sorci, Heather Vanselous, Samuel Murail, Stephanie E. Sanders, Erol Licsandru, Yves-Marie Legrand, Arie van der Lee, Poul B. Petersen, et al.(2018). Oriented chiral water wires in artificial transmembrane channels . Science Advances. 4. (3). American Association for the Advancement of Science ({AAAS})
Marc Baaden, Fabio Sterpone, Sébastien Doutreligne, Thanh Thuy Tran, Simone Melchionna, Phuong H. Nguyen, Philippe Derreumaux(2018). Multi-scale simulations of biological systems using the OPEP coarse-grained model . Biochemical and Biophysical Research Communications. 498. (2). p. 296--304. Elsevier {BV}
Marc Baaden, Ahmad Elbahnsi, Romain Retureau, Brigitte Hartmann, Christophe Oguey(2018). Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution . Journal of Chemical Theory and Computation. 14. (2). p. 1045--1058. American Chemical Society ({ACS})
Marc Baaden, Mihail Barboiu, Roslyn M. Bill, Serena Casanova, Chun-Long Chen, Matthew Conner, Viatcheslav Freger, Bing Gong, Artur Góra, Bruce Hinds, et al.(2018). Structure and function of natural proteins for water transport: general discussion . Faraday Discussions. 209. p. 83--95. Royal Society of Chemistry ({RSC})
Marc Baaden, Samuel Murail, Tudor Vasiliu, Andrei Neamtu, Mihail Barboiu, Fabio Sterpone(2018). Water permeation across artificial I-quartet membrane channels: from structure to disorder . Faraday Discussions. 209. p. 125--148. Royal Society of Chemistry ({RSC})
Marc Baaden, Manash Pratim Borthakur, Serena Casanova, Rob Coalson, Viatcheslav Freger, Miguel Gonzalez, Artur Góra, Bruce Hinds, Wisit Hirunpinyopas, Gerhard Hummer, et al.(2018). The modelling and enhancement of water hydrodynamics: general discussion . Faraday Discussions. 209. p. 273--285. Royal Society of Chemistry ({RSC})
Marc Baaden, Mihail Barboiu, Manash Pratim Borthakur, Chun-Long Chen, Rob Coalson, Jeffery Davis, Viatcheslav Freger, Bing Gong, Claus Hélix-Nielsen, Robert Hickey, et al.(2018). Applications to water transport systems: general discussion . Faraday Discussions. 209. p. 389--414. Royal Society of Chemistry ({RSC})
Marc Baaden, Mihail Barboiu, Roslyn M. Bill, Chun-Long Chen, Jeffery Davis, Maria Di Vincenzo, Viatcheslav Freger, Michael Fröba, Philip A. Gale, Bing Gong, et al.(2018). Biomimetic water channels: general discussion . Faraday Discussions. 209. p. 205--229. Royal Society of Chemistry ({RSC})
Marc Baaden, B. Kozlíková, M. Krone, M. Falk, N. Lindow, M. Baaden, D. Baum, I. Viola, J. Parulek, H.-C. Hege, et al.(2017). Visualization of Biomolecular Structures: State of the Art Revisited . Computer Graphics Forum. 36. (8). p. 178--204. Wiley
Marc Baaden, Dario De Vecchis, Laetitia Cavellini, Jérôme Hénin, Mickaël M. Cohen, Antoine Taly (2017). A membrane-inserted structural model of the yeast mitofusin Fzo1 . Scientific Reports.
Marc Baaden, Liuba Mazzanti, Sébastien Doutreligne, Cedric Gageat, Philippe Derreumaux, Antoine Taly, Samuela Pasquali(2017). What Can Human-Guided Simulations Bring to RNA Folding? . Biophysical Journal. 113. (2). p. 302--312. Elsevier {BV}
Marc Baaden, Shahid M. Nayeem, Francesco Oteri, Shashank Deep(2017). Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3 . The Journal of Physical Chemistry B. 121. (22). p. 5483--5498. American Chemical Society ({ACS})
Marc Baaden, Bogdan Lev, Samuel Murail, Frédéric Poitevin, Brett A. Cromer, Marc Delarue, Toby W. Allen (2017). String method solution of the gating pathways for a pentameric ligand-gated ion channel . Proceedings of the National Academy of Sciences.
Marc Baaden, M. Krone, B. Kozlíková, N. Lindow, M. Baaden, D. Baum, J. Parulek, H.-C. Hege, I. Viola(2016). Visual Analysis of Biomolecular Cavities: State of the Art . Computer Graphics Forum. 35. (3). p. 527--551. Wiley
Marc Baaden, Erol Licsandru, Istvan Kocsis, Yue-xiao Shen, Samuel Murail, Yves-Marie Legrand, Arie van der Lee, Daniel Tsai, Manish Kumar, Mihail Barboiu, et al.(2016). Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation . Journal of the American Chemical Society. 138. (16). p. 5403--5409. American Chemical Society ({ACS})
Marc Baaden, Benoist Laurent, Samuel Murail, Azadeh Shahsavar, Ludovic Sauguet, Marc Delarue(2016). Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel . Structure. 24. (4). p. 595--605. Elsevier {BV}
Marc Baaden, Benoist Laurent, Matthieu Chavent, Tristan Cragnolini, Anna Caroline E. Dahl, Samuela Pasquali, Philippe Derreumaux, Mark S.P. Sansom(2015). Epock: rapid analysis of protein pocket dynamics . Bioinformatics. 31. (9). p. 1478--1480. Oxford University Press ({OUP})
Marc Baaden, S. Perez, T. Tubiana, A. Imberty, M. Baaden(2015). Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: A video game-based computer graphic software . Glycobiology. 25. (5). p. 483--491. Oxford University Press ({OUP})
Marc Baaden, Gustavo Moraga-Cid, Ludovic Sauguet, Christèle Huon, Laurie Malherbe, Christine Girard-Blanc, Stéphane Petres, Samuel Murail, Antoine Taly, Marc Delarue, et al.(2015). Allosteric and hyperekplexic mutant phenotypes investigated on an α
<sub>1</sub>
glycine receptor transmembrane structure . Proceedings of the National Academy of Sciences. 112. (9). p. 2865--2870. Proceedings of the National Academy of Sciences
Marc Baaden, Tyler Reddy, David Shorthouse, Daniel L. Parton, Elizabeth Jefferys, Philip W. Fowler, Matthieu Chavent, Mark S.P. Sansom(2015). Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion . Structure. 23. (3). p. 584--597. Elsevier {BV}
Marc Baaden, T. Cragnolini, S. Doutreligne, Philippe Derreumaux, S. Pasquali(2015). Predicting and exploring complex nucleic acids architectures through a coarse-grained model . Journal of Biomolecular Structure and Dynamics.
Marc Baaden, Francesco Oteri, Elisabeth Lojou, Sophie Sacquin-Mora(2014). Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from <i>Aquifex aeolicus</i> and <i>Desulfovibrio fructosovorans</i> . The Journal of Physical Chemistry B. 118. (48). p. 13800--13811. American Chemical Society ({ACS})
Marc Baaden, Jonathan D. Hirst, David R. Glowacki(2014). Molecular simulations and visualization: introduction and overview . Faraday Discuss. 169. p. 9--22. Royal Society of Chemistry ({RSC})
Marc Baaden, Mian Wang, Jianyi Wang, Zhiqun Liang(2014). A Cooperative Mechanism of Clotrimazoles in P450 Revealed by the Dissociation Picture of Clotrimazole from P450 . Journal of Chemical Information and Modeling. 54. (4). p. 1218--1225. American Chemical Society ({ACS})
Marc Baaden, Matthieu Dreher, Jessica Prevoteau-Jonquet, Mikael Trellet, Marc Piuzzi, Bruno Raffin, Nicolas Ferey, Sophie Robert, Sébastien Limet, et al.(2014). ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations . Faraday Discuss. 169. p. 119--142. Royal Society of Chemistry ({RSC})
Marc Baaden, Francesco Oteri, Alexandre Ciaccafava, Anne de Poulpiquet, Elisabeth Lojou, Sophie Sacquin-Mora(2014). The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes . Phys. Chem. Chem. Phys. 16. (23). p. 11318--11322. Royal Society of Chemistry ({RSC})
Marc Baaden, Fabio Sterpone, Simone Melchionna, Pierre Tuffery, Samuela Pasquali, Normand Mousseau, Tristan Cragnolini, Yassmine Chebaro, Jean-Francois St-Pierre, Maria Kalimeri, et al.(2014). The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems . Chem. Soc. Rev. 43. (13). p. 4871--4893. Royal Society of Chemistry ({RSC})
Marc Baaden, A.-E. Molza, N. Férey, M. Czjzek, E. Le Rumeur, J.-F. Hubert, A. Tek, B. Laurent, M. Baaden, O. Delalande, et al.(2014). Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly . Faraday Discuss. 169. p. 45--62. Royal Society of Chemistry ({RSC})
Marc Baaden, Siewert J Marrink(2013). Coarse-grain modelling of protein–protein interactions . Current Opinion in Structural Biology. 23. (6). p. 878--886. Elsevier {BV}
Marc Baaden, Daniel L. Parton, Alex Tek, Mark S. P. Sansom(2013). Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations . PLoS Computational Biology. 9. (4). p. e1003034. Public Library of Science ({PLoS})
Marc Baaden, Zhihan Lv, Alex Tek, Franck Da Silva, Charly Empereur-mot, Matthieu Chavent(2013). Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges . PLoS ONE. 8. (3). p. e57990. Public Library of Science ({PLoS})
Marc Baaden, Ludovic Sauguet, Frédéric Poitevin, Samuel Murail, Catherine Van Renterghem, Gustavo Moraga-Cid, Laurie Malherbe, Andrew W Thompson, Patrice Koehl, Pierre-Jean Corringer, et al.(2013). Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels . The EMBO Journal. 32. (5). p. 728--741. Wiley
Marc Baaden, Matthieu Dreher, Marc Piuzzi, Ahmed Turki, Matthieu Chavent, Nicolas Férey, Sébastien Limet, Bruno Raffin, Sophie Robert, et al.(2013). Interactive Molecular Dynamics: Scaling up to Large Systems . Procedia Computer Science. 18. p. 20--29. Elsevier {BV}
M. Baaden, M. Delarue(2013). Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallography . ESRF Highlights.
Marc Baaden, Benoist Laurent, Samuel Murail, Franck Da Silva, Pierre-Jean Corringer(2012). Modeling complex biological systems: From solution chemistry to membranes and channels . Pure and Applied Chemistry. 85. (1). p. 1--13. Walter de Gruyter {GmbH}
Prevost, M.S. and Sauguet, L. and Nury, H. and Van Renterghem, C. and Huon, C. and Poitevin, F. and Baaden, M. and Delarue, M. and Corringer, P.-J.(2012). A locally closed conformation of a bacterial pentameric proton-gated ion channel . Nature Structural and Molecular Biology. 19. (6). p. 642-649.
Prevost, Marie S., Prevost, Marie S.(2012). A locally closed conformation of a bacterial pentameric proton-gated ion channel . Nature Structural & Molecular Biology. 19. (6). p. 642-+.
Darre, Leonardo, Darre, Leonardo(2012). Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk . Journal of Chemical Theory and Computation. 8. (10). p. 3880-3894.
Darré, L. and Tek, A. and Baaden, M. and Pantano, S.(2012). Mixing atomistic and coarse grain solvation models for MD simulations: Let WT4 handle the bulk . Journal of Chemical Theory and Computation. 8. (10). p. 3880-3894.
Chavent, M. and Baaden, M. and Hénon, E. and Antonczak, S.(2012). Soon in your lecture halls, chemistry will go to Hollywood. On the appropriate use of computational resources for teaching: Molecular visualization, illustrating chemical processes and physical models | 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 . Actualite Chimique. (363). p. 42-46.
Costa, D. and Garrain, P.-A. and Baaden, M.(2012). 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.
Catoire, L.J. and Damian, M. and Baaden, M. and Guittet, É. and Banères, J.-L.(2011). 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. 50. (3). p. 191-195.
Catoire, Laurent J., Catoire, Laurent J.(2011). 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. 50. (3). p. 191-195.
Delalande, Olivier, Delalande, Olivier(2011). Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase . Biophysical Journal. 101. (6). p. 1440-1449.
Delalande, O. and Sacquin-Mora, S. and Baaden, M.(2011). Enzyme closure and nucleotide binding structurally lock guanylate kinase . Biophysical Journal. 101. (6). p. 1440-1449.
Chavent, Matthieu, Chavent, Matthieu(2011). GPU-Accelerated Atom and Dynamic Bond Visualization Using Hyperballs: A Unified Algorithm for Balls, Sticks, and Hyperboloids . Journal of Computational Chemistry. 32. (13). p. 2924-2935.
Chavent, M. and Vanel, A. and Tek, A. and Levy, B. and Robert, S. and Raffin, B. and Baaden, M.(2011). GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids . Journal of Computational Chemistry. 32. (13). p. 2924-2935.
Chavent, M. and Lévy, B. and Krone, M. and Bidmon, K. and Nominé, J. and Ertl, T. and Baaden, M.(2011). GPU-powered tools boost molecular visualization . Briefings in Bioinformatics. 12. (6). p. 689-701.
Chavent, Matthieu, Chavent, Matthieu(2011). GPU-powered tools boost molecular visualization . Briefings in Bioinformatics. 12. (6). p. 689-701.
Nury, H. and Van Renterghem, C. and Weng, Y. and Tran, A. and Baaden, M. and Dufresne, V. and Changeux, J.-P. and Sonner, J.M. and Delarue, M. and Corringer, P.-J.(2011). X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel . Nature. 469. (7330). p. 428-431.
Nury, H., Nury, H.(2011). X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel . Nature. 469. (7330). p. 428-+.
Sacquin-Mora, S., Sacquin-Mora, S.(2010). Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress . Biophysical Journal. 99. (10). p. 3412-3419.
Sacquin-Mora, S. and Delalande, O. and Baaden, M.(2010). Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress . Biophysical Journal. 99. (10). p. 3412-3419.
Sacquin-Mora, S., Sacquin-Mora, S.(2010). Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress . Biophysical Journal. 99. (10). p. 3412-3419.
Gueroult, M., Gueroult, M.(2010). How Cations Can Assist DNase I in DNA Binding and Hydrolysis . Plos Computational Biology. 6. (11).
Gueroult, Marc, Gueroult, Marc(2010). How Cations Can Assist DNase I in DNA Binding and Hydrolysis . Plos Computational Biology. 6. (11).
Guéroult, M. and Picot, D. and Abi-Ghanem, J. and Hartmann, B. and Baaden, M.(2010). How cations can assist dnase i in DNA binding and hydrolysis . PLoS Computational Biology. 6. (11).
Saladin, A. and Amourda, C. and Poulain, P. and Férey, N. and Baaden, M. and Zacharias, M. and Delalande, O. and Prévost, C.(2010). Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments . Nucleic Acids Research. 38. (19). p. 6313-6323.
Saladin, A., Saladin, A.(2010). Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments . Nucleic Acids Research. 38. (19). p. 6313-6323.
Delalande, Olivier, Delalande, Olivier(2010). 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. Pacific Symposium on Biocomputing. p. 205-15.
Nury, H. and Poitevin, F. and Van Renterghem, C. and Changeux, J.-P. and Corringer, P.-J. and Delarue, M. and Baaden, M.(2010). 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. 107. (14). p. 6275-6280.
Nury, H., Nury, H.(2010). 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. 107. (14). p. 6275-6280.
Sinha, D. K., Sinha, D. K.(2010). Photocontrol of Protein Activity in Cultured Cells and Zebrafish with One- and Two-Photon Illumination . Chembiochem. 11. (5). p. 653-663.
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.(2010). Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination . ChemBioChem. 11. (5). p. 653-663.
Zhang, Y. B., Zhang, Y. B.(2010). 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. 114. (43). p. 13839-13846.
Zhang, Y. and Baaden, M. and Yan, J. and Shao, J. and Qiu, S. and Wu, Y. and Ding, Y.(2010). The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif . Journal of Physical Chemistry B. 114. (43). p. 13839-13846.
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.(2010). Atomic structure and dynamics of pentameric ligand-gated ion channels: New insight from bacterial homologues . Journal of Physiology. 588. (4). p. 565-572.
Corringer, P. J., Corringer, P. J.(2010). Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues . Journal of Physiology-London. 588. (4). p. 565-572.
Durrieu, M. P., Durrieu, M. P.(2009). Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States . Chemphyschem. 10. (9-10). p. 1548-1552.
Durrieu, M.-P. and Bond, P.J. and Sansom, M.S.P. and Lavery, R. and Baaden, M.(2009). Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states . ChemPhysChem. 10. (9-10). p. 1548-1552.
Delalande, O., Delalande, O.(2009). Complex Molecular Assemblies at Hand via Interactive Simulations . Journal of Computational Chemistry. 30. (15). p. 2375-2387.
Delalande, O. and Férey, N. and Grasseau, G. and Baaden, M.(2009). Complex molecular assemblies at hand via interactive simulations . Journal of Computational Chemistry. 30. (15). p. 2375-2387.
Bocquet, N., Nury, H., Baaden, M., Le Poupon, C., Changeux, J.-P., Delarue, M., Corringer, P.-J., Bocquet, N., Nury, H., Baaden, M., et al.(2009). X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation . Nature. 457. (7225). p. 111-114.
Bocquet, N., Bocquet, N.(2009). X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation . Nature. 457. (7225). p. 111-114.
Férey, N. and Delalande, O. and Grasseau, G. and Baaden, M.(2008). A VR framework for interacting with molecular simulations . Proceedings of the ACM Symposium on Virtual Reality Software and Technology, VRST. p. 91-94.
Durrieu, M.-P. and Lavery, R. and Baaden, M.(2008). Interactions between neuronal fusion proteins explored by molecular dynamics . Biophysical Journal. 94. (9). p. 3436-3446.
Durrieu, M. P., Durrieu, M. P.(2008). Interactions between neuronal fusion proteins explored by molecular dynamics . Biophysical Journal. 94. (9). p. 3436-3446.
Neri, M. and Baaden, M. and Carnevale, V. and Anselmi, C. and Maritan, A. and Carloni, P.(2008). Microseconds dynamics simulations of the outer-membrane protease T . Biophysical Journal. 94. (1). p. 71-78.
Neri, M., Neri, M.(2008). Microseconds dynamics simulations of the outer-membrane protease T . Biophysical Journal. 94. (1). p. 71-78.
Cox, K. and Bond, P.J. and Grottesi, A. and Baaden, M. and Sansom, M.S.P.(2008). Outer membrane proteins: Comparing X-ray and NMR structures by MD simulations in lipid bilayers . European Biophysics Journal. 37. (2). p. 131-141.
Cox, K., Cox, K.(2008). Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers . European Biophysics Journal with Biophysics Letters. 37. (2). p. 131-141.
Tai, K. and Baaden, M. and Murdock, S. and Wu, B. and Ng, M.H. and Johnston, S. and Boardman, R. and Fangohr, H. and Cox, K. and Essex, J.W. and Sansom, M.S.P.(2007). Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database . Journal of Molecular Graphics and Modelling. 25. (6). p. 896-902.
Tai, K., Tai, K.(2007). Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database . Journal of Molecular Graphics & Modelling. 25. (6). p. 896-902.
Tai, Kaihsu, Tai, Kaihsu(2007). Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database . Journal of Molecular Graphics & Modelling. 25. (6). p. 896-902.
Law, R.J. and Capener, C. and Baaden, M. and Bond, P.J. and Campbell, J. and Patargias, G. and Arinaminpathy, Y. and Sansom, M.S.P.(2005). Membrane protein structure quality in molecular dynamics simulation . Journal of Molecular Graphics and Modelling. 24. (2). p. 157-165.
Law, R. J., Law, R. J.(2005). Membrane protein structure quality in molecular dynamics simulation . Journal of Molecular Graphics & Modelling. 24. (2). p. 157-165.
Faraldo-Gomez, J. D., Faraldo-Gomez, J. D.(2004). Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations . Proteins-Structure Function and Bioinformatics. 57. (4). p. 783-791.
Baaden, M., Baaden, M.(2004). OmpT: Molecular dynamics simulations of an outer membrane enzyme . Biophysical Journal. 87. (5). p. 2942-2953.
Baaden, M. and Sansom, M.S.P.(2004). OmpT: Molecular dynamics simulations of an outer membrane enzyme . Biophysical Journal. 87. (5). p. 2942-2953.
Baaden, M., Baaden, M.(2004). OmpT: Molecular dynamics simulations of an outer membrane enzyme . Biophysical Journal. 87. (5). p. 2942-2953.
Faraldo-Gómez, J.D. and Forrest, L.R. and Baaden, M. and Bond, P.J. and Domene, C. and Patargias, G. and Cuthbertson, J. and Sansom, M.S.P.(2004). Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations . Proteins: Structure, Function and Genetics. 57. (4). p. 783-791.
Baaden, M. and Meier, C. and Sansom, M.S.P.(2003). A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA . Journal of Molecular Biology. 331. (1). p. 177-189.
Baaden, M., Baaden, M.(2003). A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA . Journal of Molecular Biology. 331. (1). p. 177-189.
Baaden, M. and Meier, C. and Sansom, M.S.P.(2003). A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA . Journal of Molecular Biology. 331. (1). p. 177-189.
Campbell, J.D. and Biggin, P.C. and Baaden, M. and Sansom, M.S.P.(2003). Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA . Biochemistry. 42. (13). p. 3666-3673.
Campbell, J. D., Campbell, J. D.(2003). Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA . Biochemistry. 42. (13). p. 3666-3673.
Baaden, M. and Berny, F. and Madic, C. and Schurhammer, R. and Wipff, G.(2003). Theoretical studies on Lanthanide cation extraction by picolinamides: Ligand-Cation interactions and interfacial behavior . Solvent Extraction and Ion Exchange. 21. (2). p. 199-220.
Baaden, M., Baaden, M.(2003). Theoretical studies on lanthanide cation extraction by picolinamides: Ligand-cation interactions and interfacial behavior . Solvent Extraction and Ion Exchange. 21. (2). p. 199-220.
Baaden, M., Baaden, M.(2002). Barrels & corks in a computer - Modelling bacterial iron transport systems. Biophysical Journal. 82. (1). p. 2610.
Baaden, M. and Schurhammer, R. and Wipff, G.(2002). Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/ . Journal of Physical Chemistry B. 106. (2). p. 434-441.
Baaden, M., Baaden, M.(2002). Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/"oil"/TBP solutions with a comparison of supercritical CO2 and chloroform . Journal of Physical Chemistry B. 106. (2). p. 434-441.
Baaden, M. and Burgard, M. and Boehme, C. and Wipff, G.(2001). 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). p. 1317-1325.
Baaden, M. and Burgard, M. and Boehme, C. and Wipff, G.(2001). 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). p. 1317-1325.
Baaden, M. and Burgard, M. and Wipff, G.(2001). 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). p. 11131-11141.
Baaden, M., Baaden, M.(2001). 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). p. 11131-11141.
Baaden, M. and Berny, F. and Wipff, G.(2001). The chloroform / TBP / aqueous nitric acid interfacial system: A molecular dynamics investigation . Journal of Molecular Liquids. 90. (1-3). p. 1-9.
Lambert, B. and Jacques, V. and Shivanyuk, A. and Matthews, S.E. and Tunayar, A. and Baaden, M. and Wipff, G. and Böhmer, V. and Desreux, J.F.(2000). 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). p. 2033-2041.
Lambert, B., Lambert, B.(2000). 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). p. 2033-2041.
Baaden, M. and Wipff, G. and Yaftian, M.R. and Burgard, M. and Matt, D.(2000). 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). p. 1315-1321.
Baaden, M., Baaden, M.(2000). 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). p. 1315-1321.
Baaden, M., Baaden, M.(2000). 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). p. 1315-1321.
Troxler, L. and Baaden, M. and Böhmer, V. and Wipff, G.(2000). 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). p. 27-51.
Troxler, L. and Baaden, M. and Böhmer, V. and Wipff, G.(2000). 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). p. 27-51.
Baaden, M. and Granger, P. and Strich, A.(2000). 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 2C=CH-X . Molecular Physics. 98. (6). p. 329-342.
Baaden, M., Baaden, M.(2000). 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). p. 329-342.
Baaden, M.(2000). Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: A quantum mechanics study . Journal of Alloys and Compounds. 303-304. p. 104-111.
Baaden, M., Baaden, M.(2000). Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study. Journal of Alloys and Compounds. 303. p. 104-111.
Baaden, M. and Berny, F. and Muzet, N. and Troxler, L. and Wipff, G.(2000). Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: A molecular dynamics investigation . ACS Symposium Series. 757. p. 71-85.
Baaden, M. and Berny, F. and Muzet, N. and Troxler, L. and Wipff, G.(2000). Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: A molecular dynamics investigation . ACS Symposium Series. 757. p. 71-85.
Baaden, M., Baaden, M.(2000). 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). p. 7659-7671.
Baaden, M. and Berny, F. and Madic, C. and Wipff, G.(2000). 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). p. 7659-7671.
Baaden, M. and Berny, F. and Madic, C. and Wipff, G.(2000). 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). p. 7659-7671.
PREPRINT
Marc Baaden, Diego Barquero Morera, Giovanni Mattiotti, Alexander Kocev, Amshuman Rousselot, Louis Meuret, Lucas Rouaud, Hubert Santuz, Antoine Taly, Samuela Pasquali (2025). Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein Binding Pockets .
Marc Baaden, Baptiste Etcheverry, Aurélien de la Lande, Fabien Cailliez (2025). NOX transmembrane electron transfer is governed by a subtly balanced, self-adjusting charge distribution .
Marc Baaden, Johanna K. S. Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J. Howard, Lucie Delemotte, Erik Lindahl, Kresten Lindorff-Larsen, et al. (2024). MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations .
Marc Baaden, Raphaëlle Versini, Laetitia Cavellini, Mickaël M. Cohen, Antoine Taly, Patrick F.J. Fuchs (2023). Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion .
Marc Baaden, Johanna K. S. Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J. Howard, Lucie Delemotte, Erik Lindahl, Kresten Lindorff-Larsen, et al. (2023). MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations .
Marc Baaden, Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas, Thibault TUBIANA, Sana Zineb Aimeur, Julien HENRI, Marie Erard, Oliver Nüsse, ANDREANI Jessica, et al. (2023). A Perspective on the Prospective Use of AI in Protein Structure Prediction .
Marc Baaden, Johanna K. S. Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J. Howard, Lucie Delemotte, Erik Lindahl, Kresten Lindorff-Larsen, et al. (2023). MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations .
Marc Baaden, Xavier Martinez (2020). FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments .
BOOK CHAPTER
Marc Baaden, Iza Marfisi, Hubert Santuz, Camille Bisson, Nicolas Férey, Antoine Taly, Olivier Delalande (2025). Escape from PharmaZ: A Game to Boost Pharmacophore Learning Through Immersive Augmented Reality .
Marc Baaden, A. Hardiagon, S. Murail, L. Huang, M. Barboiu, F. Sterpone, M. Baaden(2021). Stability and Structure of Adaptive Self-organized Supramolecular Artificial Water Channels in Lipid Bilayers . New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications. p. 51--63. Springer International Publishing
Marc Baaden, Xavier Martinez, Arthur Hardiagon, Hubert Santuz, Samuel Murail, Mihail Barboiu, Fabio Sterpone(2020). Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels . Advances in Bionanomaterials II. p. 78--99. Springer International Publishing
Marc Baaden (2020). Computer Simulations Provide Guidance for Molecular Medicine Through Insights on Dynamics and Mechanisms at the Atomic Scale .
Marc Baaden, Jérôme Hénin, Antoine Taly(2014). 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. p. 347--392. Springer New York
Marc Baaden, Alex Tek, Matthieu Chavent, Olivier Delalande, Patrick Bourdot, Brian FG Katz, Nicolas Ferey(2012). Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations . Protein-Protein Interactions - Computational and Experimental Tools. {IntechOpen}
Marc Baaden, Syma Khalid(2010). Chapter 9. Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels . RSC Biomolecular Sciences. p. 225--247. Royal Society of Chemistry
Marc Baaden, Richard Lavery(2007). There's plenty of room in the middle: Multiscale Modelling of Biological Systems .
CONFERENCE PAPER
Marc Baaden, Rajkumar Darbar, Hubert Santuz, Antoine Taly (2024). GazeMolVR: Sharing Eye-Gaze Cues in a Collaborative VR Environment for Molecular Visualization .
Marc Baaden, Mikael Trellet, Nicolas Ferey, Patrick Bourdot(2016). Interactive visual analytics of molecular data in immersive environments via a semantic definition of the content and the context . 2016 Workshop on Immersive Analytics (IA). {IEEE}
Marc Baaden, Mikael Trellet, Nicolas Ferey, Patrick Bourdot(2015). Content and task based navigation for structural biology in 3D environments . 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR). {IEEE}
Marc Baaden, Sebastien Doutreligne, Cedric Gageat, Tristan Cragnolini, Antoine Taly, Samuela Pasquali, Philippe Derreumaux(2015). UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules . 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR). {IEEE}
Marc Baaden, Barbora Kozlikova, Michael Krone, Norbert Lindow, Martin Falk, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege, et al.(2015). Visualization of Biomolecular Structures: State of the Art . Eurographics Conference on Visualization (EuroVis) - STARs. The Eurographics Association
Content-guided Navigation in Multimeric Molecular Complexes @inproceedings{2014, doi = {10.5220/0004914300760081}, url = {https://doi.org/10.5220%2F0004914300760081}, year = 2014, publisher = {{SCITEPRESS} - Science and and Technology Publications}, title = {Content-guided Navigation in Multimeric Molecular Complexes}, booktitle = {Proceedings of the International Conference on Bioimaging}} . Proceedings of the International Conference on Bioimaging.
M. Trellet, N. Férey, M. Baaden, P. Bourdot(2013). Navigation guidée par le contenu pour l'exploration moléculaire .
Marc Baaden, Nicolas Férey, Olivier Delalande, Gilles Grasseau(2008). From Interactive to Immersive Molecular Dynamics . Workshop in Virtual Reality Interactions and Physical Simulation "VRIPHYS" (2008). The Eurographics Association
OTHER
Marc Baaden, Nicolas Bourassin, Florent Barbault, Sophie Sacquin-Mora(2021). Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces . Cold Spring Harbor Laboratory
Marc Baaden, Nicolas Bourassin, Florent Barbault, Sophie Sacquin-Mora(2021). Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces . Cold Spring Harbor Laboratory
NEWSPAPER ARTICLE
Marc Baaden, Naif Alharbi, Mohammad Alharbi, Xavier Martinez, Michael Krone, Alexander S. Rose, Robert S. Laramee, Matthieu Chavent(2017). Molecular Visualization of Computational Biology Data: A Survey of Surveys . EuroVis 2017 - Short Papers. The Eurographics Association
WORKING PAPER
BOOK
Marc Baaden, Axel Kahn, Sebastien Fleuret, Sébastien Descotes-Genon, Nicolas B. Garnier, Carole Levenes, Hirac Gurden, Ina Reiche, Nicolas Ginet, Laurence Gay, et al.(2009). Itinéraires Bis .
Ratings and Comments
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