Marc Baaden

Publications

Article dans une revue (133)

Dynamic Regulation of Proton and Water Transport through an Acylhydrazone-Based Photoresponsive Channel Paras Wanjari,Ioan Stroia,Arie van der Lee,Marc Baaden,Mihail Barboiu Journal of the American Chemical Society, 2025, 147 (39), pp.35264-35274. ⟨10.1021/jacs.5c05942⟩ Article dans une revue hal-05359382v1
Virtual reality in drug design: Benefits, applications and industrial perspectives Marc Baaden,David R Glowacki Current Opinion in Structural Biology, 2025, 92, pp.103044. ⟨10.1016/j.sbi.2025.103044⟩ Article dans une revue hal-05024222v1
Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets Diego Barquero Morera,Giovanni Mattiotti,Alexandar Kocev,Amshuman Rousselot,Louis Meuretet al. Journal of Chemical Theory and Computation, 2025, ⟨10.1021/acs.jctc.5c00688⟩ Article dans une revue hal-05236200v1
NOX Transmembrane Electron Transfer Is Governed by a Subtly Balanced, Self-Adjusting Charge Distribution Baptiste Etcheverry,Marc Baaden,Aurélien de la Lande,Fabien Cailliez Journal of Chemical Information and Modeling, 2025, 65 (15), pp.8215-8228. ⟨10.1021/acs.jcim.5c00746⟩ Article dans une revue hal-05227867v1
State-dependent dynamic communication networks in a pentameric ligand-gated ion channel Bogdan Lev,Samuel Murail,Igor Vorobyov,Marc Baaden,Toby Allen Journal of Physical Chemistry B, 2025, 129 (37), pp.9333-9356. ⟨10.1021/acs.jpcb.5c03991⟩ Article dans une revue hal-05412186v1
BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics Benoist Laurent,André Lanrezac,Hubert Santuz,Nicolas Ferey,Olivier Delalandeet al. Protein Science, 2025, 34 (5), pp.e70130. ⟨10.1002/pro.70130⟩ Article dans une revue hal-05039981v1
MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform Marc Baaden Journal of Physical Chemistry B, 2024, 128 (38), pp.9132-9142. ⟨10.1021/acs.jpcb.4c04712⟩ Article dans une revue hal-04794544v1
Water-Pore Flow Permeation through Multivalent H-Bonding Pyridine-2,6-dicarboxamide-histamine/Histidine Water Channels Li-Bo Huang,Dan-Dan Su,Arthur Hardiagon,Istvan Kocsis,Arie van der Leeet al. Journal of the American Chemical Society, 2024, 147 (1), pp.678-686. ⟨10.1021/jacs.4c13072⟩ Article dans une revue hal-05022271v1
A Perspective on the prospective use of AI in protein structure prediction Raphaelle Versini,Sujith Sritharan,Burcu Aykaç Fas,Thibault Tubiana,Sana Zineb Aimeuret al. Journal of Chemical Information and Modeling, 2024, 64 (1), pp.26-41. ⟨10.1021/acs.jcim.3c01361⟩ Article dans une revue hal-04306436v1
From complex data to clear insights: visualizing molecular dynamics trajectories Hayet Belghit,Mariano Spivak,Manuel Dauchez,Marc Baaden,Jessica Jonquet-Prevoteau Frontiers in Bioinformatics, 2024, 4, ⟨10.3389/fbinf.2024.1356659⟩ Article dans une revue hal-04568346v1
Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion Raphaëlle Versini,Marc Baaden,Laetitia Cavellini,Mickaël M Cohen,Antoine Talyet al. Structure, 2024, 32 (11), pp.1997-2012.e7. ⟨10.1101/2023.09.22.559002⟩ Article dans une revue hal-04299450v1
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations Johanna K S Tiemann,Magdalena Szczuka,Lisa Bouarroudj,Mohamed Oussaren,Steven Garciaet al. eLife, 2023, ⟨10.7554/elife.90061⟩ Article dans une revue hal-04254566v2
Combinatorial Screening of Water/Proton Permeation of Self‐Assembled Pillar[5]arene Artificial Water Channel Libraries Iuliana-Marilena Andrei,Dmytro Strilets,Shixin Fa,Marc Baaden,Tomoki Ogoshiet al. Angewandte Chemie International Edition, 2023, 62 (42), pp.e202310812. ⟨10.1002/anie.202310812⟩ Article dans une revue hal-04257786v1
UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape André Lanrezac,Marc Baaden Membranes, 2023, 13 (3), pp.362. ⟨10.3390/membranes13030362⟩ Article dans une revue hal-04306427v1
Proton- versus Cation-Selective Transport of Saccharide Rim-Appended Pillar[5]arene Artificial Water Channels Iuliana M Andrei,Wenzhang Chen,Marc Baaden,Stéphane P Vincent,Mihai Barboiu Journal of the American Chemical Society, 2023, 145 (40), pp.21904-21914. ⟨10.1021/jacs.3c06335⟩ Article dans une revue hal-04257737v1
Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT Yubo Zhang,Marc Baaden Catalysts, 2023, 13 (2), pp.214. ⟨10.3390/catal13020214⟩ Article dans une revue hal-03943290v1
State of the Art of Molecular Visualization in Immersive Virtual Environments David Kuťák,Pere‐pau Vázquez,Tobias Isenberg,Michael Krone,Marc Baadenet al. Computer Graphics Forum, 2023, 42 (6), pp.e14738:1--e14738:29. ⟨10.1111/cgf.14738⟩ Article dans une revue hal-04006531v1
A brief history of visualizing membrane systems in molecular dynamics simulations Robin A Corey,Marc Baaden,Matthieu Chavent Frontiers in Bioinformatics, 2023, 3, pp.1149744. ⟨10.3389/fbinf.2023.1149744⟩ Article dans une revue hal-04306431v1
Self-Assembling Peptide-Appended Metallomacrocycle Pores for Selective Water Translocation Li-Bo Huang,Fumihiko Mamiya,Marc Baaden,Eiji Yashima,Mihail Barboiu ACS Applied Materials & Interfaces, 2023, 15 (33), pp.40133-40139. ⟨10.1021/acsami.3c09059⟩ Article dans une revue hal-04257762v1
Fast and Interactive Positioning of Proteins within Membranes André Lanrezac,Benoist Laurent,Hubert Santuz,Nicolas Férey,Marc Baaden Algorithms, 2022, 15 (11), pp.415. ⟨10.3390/a15110415⟩ Article dans une revue hal-03873725v1
Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design Björn Sommer,Daisuke Inoue,Marc Baaden Journal of Integrative Bioinformatics, 2022, 19 (2), ⟨10.1515/jib-2022-0037⟩ Article dans une revue hal-03873706v1
Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces Nicolas Bourassin,Florent Barbault,Marc Baaden,Sophie Sacquin-Mora Langmuir, 2022, 38 (4), pp.1313-1323. ⟨10.1021/acs.langmuir.1c01774⟩ Article dans une revue hal-03294641v1
A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study Staëlle Makamte,Aurélien Thureau,Amira Jabrani,Annick Paquelin,Anne Plessiset al. Journal of Structural Biology, 2022, 214 (2), pp.107853. ⟨10.1016/j.jsb.2022.107853⟩ Article dans une revue hal-03413156v1
Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies Anne-Elisabeth Molza,Yvonne Westermaier,Magali Moutte,Pierre Ducrot,Claudia Danilowiczet al. Frontiers in Molecular Biosciences, 2022, 9, pp.826136. ⟨10.3389/fmolb.2022.826136⟩ Article dans une revue hal-03826944v1
Artificial Water Channels Form Precursors to Sponge-Like Aggregates in Water–Ethanol Mixtures Arthur Hardiagon,Marc Baaden,Fabio Sterpone Journal of Physical Chemistry A, 2022, 126 (38), pp.6628-6636. ⟨10.1021/acs.jpca.2c04545⟩ Article dans une revue hal-03873715v1
Deep inside molecules - digital twins at the nanoscale Marc Baaden Virtual Reality & Intelligent Hardware, 2022, 4, pp.324 - 341. ⟨10.1016/j.vrih.2022.03.001⟩ Article dans une revue hal-03873710v1
Design – a new way to look at old molecules Davide Spalvieri,Anne-Marine Mauviel,Matthieu Lambert,Nicolas Férey,Sophie Sacquin-Moraet al. Journal of Integrative Bioinformatics, 2022, 19 (2), pp.20220020. ⟨10.1515/jib-2022-0020⟩ Article dans une revue hal-03793308v1
UnityMol prototype for FAIR sharing of molecular- visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments Xavier Martinez,Marc Baaden Acta crystallographica Section D : Structural biology [1993-..], 2021, 77 (6), pp.746-754. ⟨10.1107/S2059798321002941⟩ Article dans une revue hal-02944943v2
Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic Núria López,Luigi del Debbio,Marc Baaden,Matej Praprotnik,Laura Grigoriet al. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (46), pp.e2024891118. ⟨10.1073/pnas.2024891118⟩ Article dans une revue hal-03438495v1
Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations Xiaojing Wu,Jérôme Hénin,Laura Baciou,Marc Baaden,Fabien Cailliezet al. Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩ Article dans une revue hal-03382660v1
The never-ending quest to understand the shapes and motions of molecules Marc Baaden The Biochemist, 2021, 43 (5), pp.22-24. ⟨10.1042/bio_2021_175⟩ Article dans une revue hal-03438490v1
Wielding the power of interactive molecular simulations André Lanrezac,Nicolas Férey,Marc Baaden Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021, 12 (4), pp.e1594. ⟨10.1002/WCMS.1594⟩ Article dans une revue hal-03447181v1
Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs Arthur Hardiagon,Samuel Murail,Li-Bo Huang,Arie van Der Lee,Fabio Sterponeet al. The Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩ Article dans une revue hal-03410227v1
Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation Li-Bo Huang,Arthur Hardiagon,Istvan Kocsis,Cristina-Alexandra Jegu,Mihai Deleanuet al. Journal of the American Chemical Society, 2021, 143 (11), pp.4224-4233. ⟨10.1021/jacs.0c11952⟩ Article dans une revue hal-03364954v2
Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grain Representation Nicolas Bourassin,Marc Baaden,Elisabeth Lojou,Sophie Sacquin-Mora Journal of Physical Chemistry B, 2020, 15, ⟨10.1021/acs.jpcb.0c05347⟩ Article dans une revue hal-02939019v1
Characterization of β-turns by electronic circular dichroism spectroscopy: A coupled molecular dynamics and time-dependent density functional theory computational study Mattia Migliore,Andrea Bonvicini,Vincent Tognetti,Laure Guilhaudis,Marc Baadenet al. Physical Chemistry Chemical Physics, 2020, 22 (3), pp.1611-1623. ⟨10.1039/C9CP05776E⟩ Article dans une revue hal-02397135v1
Visualizing protein structures - tools and trends Xavier Martinez,Matthieu Chavent,Marc Baaden Biochemical Society Transactions, 2020, 48 (2), pp.499-506. ⟨10.1042/BST20190621⟩ Article dans une revue hal-02946006v1
Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers Dmytro Strilets,Shixin Fa,Arthur Hardiagon,Marc Baaden,Tomoki Ogoshiet al. Angewandte Chemie International Edition, 2020, 59 (51), pp.23213-23219. ⟨10.1002/anie.202009219⟩ Article dans une revue hal-03028876v1
Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS Joseph Laureanti,Juan Brandi,Elvis Offor,David Engel,Robert Ralloet al. Protein Science, 2020, 29 (1), pp.237-246. ⟨10.1002/pro.3773⟩ Article dans une revue hal-02370955v1
Scruter les molécules en réalité virtuelle, pour quoi faire ? Xavier Martinez,Marc Baaden L'Actualité Chimique, 2020, 448, pp.23-26 Article dans une revue hal-02946000v1
Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching Antoine Taly,F. Nitti,Marc Baaden,S. Pasquali Interface Focus, 2019, 9 (3), pp.20180065. ⟨10.1098/rsfs.2018.0065⟩ Article dans une revue hal-02345057v1
Glutathionylation primes soluble GAPDH for late collapse into insoluble aggregates Mirko Zaffagnini,Christophe H. Marchand,M. Malferrari,Samuel Murail,Sara Bonacchiet al. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (51), pp.26057-26065. ⟨10.1073/pnas.1914484116⟩ Article dans une revue hal-02370717v1
Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics Astrid F. Brandner,Stepan Timr,Simone Melchionna,Philippe Derreumaux,Marc Baadenet al. Scientific Reports, 2019, 9, pp.16450. ⟨10.1038/s41598-019-52760-y⟩ Article dans une revue hal-02370975v1
A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin Dario de Vecchis,Astrid Brandner,Marc Baaden,Mickaël M Cohen,Antoine Taly Journal of Membrane Biology, 2019, 252 (4-5), pp.293-306. ⟨10.1007/s00232-019-00089-y⟩ Article dans une revue hal-02345040v1
Molecular Graphics: Bridging Structural Biologists and Computer Scientists Xavier Martinez,Michael Krone,Naif Alharbi,Alexander Rose,Robert Larameeet al. Structure, 2019, 27 (11), pp.1617-1623. ⟨10.1016/j.str.2019.09.001⟩ Article dans une revue hal-02370947v1
Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking Astrid Brandner,Dario de Vecchis,Marc Baaden,Mickaël M Cohen,Antoine Taly Data in Brief, 2019, 26, pp.104460. ⟨10.1016/j.dib.2019.104460⟩ Article dans une revue hal-02345034v1
Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking Astrid Brandner,Dario de Vecchis,Marc Baaden,Mickaël M Cohen,Antoine Taly Mitochondrion, 2019, 49, pp.234-244. ⟨10.1016/j.mito.2019.06.010⟩ Article dans une revue hal-02345043v1
Visualizing Biological Membrane Organization and Dynamics Marc Baaden Journal of Molecular Biology, 2019, 431 (10), pp.1889-1919. ⟨10.1016/j.jmb.2019.02.018⟩ Article dans une revue hal-02370047v1
Biomimetic water channels: general discussion Marc Baaden,Mihail Barboiu,Roslyn Bill,Chun-Long Chen,Jeffery Daviset al. Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩ Article dans une revue hal-01926861v1
Oriented chiral water wires in artificial transmembrane channels Istvan Kocsis,Mirco Sorci,Heather Vanselous,Samuel Murail,Stephanie Sanderset al. Science Advances , 2018, 4 (3), pp.eaao5603. ⟨10.1126/sciadv.aao5603⟩ Article dans une revue hal-01797309v1
Water permeation across artificial I-quartet membrane channels: from structure to disorder Samuel Murail,Tudor Vasiliu,Andrei Neamtu,Mihail Barboiu,Fabio Sterponeet al. Faraday Discussions, 2018, 209, pp.125 - 148. ⟨10.1039/c8fd00046h⟩ Article dans une revue hal-01926847v1
Ten simple rules to create a serious game, illustrated with examples from structural biology Marc Baaden,Olivier Delalande,Nicolas Ferey,Samuela Pasquali,Jérôme Waldispühlet al. PLoS Computational Biology, 2018, 14 (3), pp.e1005955. ⟨10.1371/journal.pcbi.1005955⟩ Article dans une revue hal-01744190v1
Applications to water transport systems: general discussion Marc Baaden,Mihail Barboiu,Manash Pratim Borthakur,Chun-Long Chen,Rob Coalsonet al. Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩ Article dans une revue hal-01926896v1
Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data Mikael Trellet,Nicolas Ferey,Jakub Flotyński,Marc Baaden,Patrick Bourdot Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180004. ⟨10.1515/jib-2018-0004⟩ Article dans une revue hal-01935586v1
Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution Ahmad Elbahnsi,Romain Retureau,Marc Baaden,Brigitte Hartmann,Christophe Oguey Journal of Chemical Theory and Computation, 2018, 14 (2), pp.1045 - 1058. ⟨10.1021/acs.jctc.7b00936⟩ Article dans une revue hal-01935581v1
Multi-scale simulations of biological systems using the OPEP coarse-grained model Fabio Sterpone,Sébastien Doutreligne,Thanh Thuy Tran,Simone Melchionna,Marc Baadenet al. Biochemical and Biophysical Research Communications, 2018, 498 (2), pp.296-304. ⟨10.1016/j.bbrc.2017.08.165⟩ Article dans une revue hal-01644564v1
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis Alexandre Maes,Xavier Martinez,Karen Druart,Benoist Laurent,Sean Guéganet al. Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180006. ⟨10.1515/jib-2018-0006⟩ Article dans une revue hal-01935585v1
Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network Jeremy Esque,Mark S. P. Sansom,Marc Baaden,Christophe Oguey Scientific Reports, 2018, 8, pp.13540. ⟨10.1038/s41598-018-31422-5⟩ Article dans une revue hal-01883877v1
Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions Olivier Delalande,Anne-Elisabeth Molza,Raphael dos Santos Morais,Angélique Chéron,Emeline Polletet al. Journal of Biological Chemistry, 2018, 293 (18), pp.6637-6646. ⟨10.1074/jbc.M117.809798⟩ Article dans une revue hal-01795395v2
From Virtual Reality to Immersive Analytics in Bioinformatics Björn Sommer,Marc Baaden,Michael Krone,Andrew Woods Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180043. ⟨10.1515/jib-2018-0043⟩ Article dans une revue hal-01935682v1
Controlling Redox Enzyme Orientation at Planar Electrodes Vivek Pratap Hitaishi,Romain Clément,Nicolas Bourassin,Marc Baaden,Anne de Poulpiquetet al. Catalysts, 2018, 8 (5), pp.192. ⟨10.3390/catal8050192⟩ Article dans une revue hal-01793660v1
The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo Jens-Christian M Röper,Démosthène Mitrossilis,Guillaume Stirnemann,François Waharte,Isabel Britoet al. eLife, 2018, 7, ⟨10.7554/eLife.33381⟩ Article dans une revue hal-01935588v1
Structure and function of natural proteins for water transport: general discussion Marc Baaden,Mihail Barboiu,Roslyn Bill,Serena Casanova,Chun-Long Chenet al. Faraday Discussions, 2018, 209, pp.83 - 95. ⟨10.1039/C8FD90019A⟩ Article dans une revue hal-01926768v1
A membrane-inserted structural model of the yeast mitofusin Fzo1 Dario de Vecchis,Laetitia Cavellini,Marc Baaden,Jérôme Hénin,Mickaël M. Cohenet al. Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩ Article dans une revue hal-01581980v1
What Can Human-Guided Simulations Bring to RNA Folding? Liuba Mazzanti,Sébastien Doutreligne,Cédric Gageat,Philippe Derreumaux,Antoine Talyet al. Biophysical Journal, 2017, 113 (2), pp.302 - 312. ⟨10.1016/j.bpj.2017.05.047⟩ Article dans une revue hal-01644519v1
Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3 Shahid M. Nayeem,Francesco Oteri,Marc Baaden,Shashank Deep Journal of Physical Chemistry B, 2017, 121 (22), pp.5483 - 5498. ⟨10.1021/acs.jpcb.7b01867⟩ Article dans une revue hal-01587914v1
String method solution of the gating pathways for a pentameric ligand-gated ion channel Bogdan Lev,Samuel Murail,Frédéric Poitevin,Brett A Cromer,Marc Baadenet al. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (21), pp.E4158 - E4167. ⟨10.1073/pnas.1617567114⟩ Article dans une revue hal-01644525v1
Visualization of Biomolecular Structures: State of the Art Revisited B. Kozlíková,M. Krone,M. Falk,N. Lindow,Marc Baadenet al. Computer Graphics Forum, 2017, 36 (8), pp.178-204. ⟨10.1111/cgf.13072⟩ Article dans une revue hal-01400465v1
Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel Benoist Laurent,Samuel Murail,Azadeh Shahsavar,Ludovic Sauguet,Marc Delarueet al. Structure, 2016, 24 (4), pp.595 - 605. ⟨10.1016/j.str.2016.02.014⟩ Article dans une revue hal-01400467v1
Visual Analysis of Biomolecular Cavities: State of the Art M. Krone,B. Kozlíková,N. Lindow,Marc Baaden,D. Baumet al. Computer Graphics Forum, 2016, 35 (3), pp.527 - 551. ⟨10.1111/cgf.12928⟩ Article dans une revue istex hal-01400464v1
Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation Erol Licsandru,Istvan Kocsis,Yue-Xiao Shen,Samuel Murail,Yves-Marie Legrandet al. Journal of the American Chemical Society, 2016, 138 (16), pp.5403 - 5409. ⟨10.1021/jacs.6b01811⟩ Article dans une revue hal-01400466v1
Epock : rapid analysis of protein pocket dynamics Benoist Laurent,Matthieu Chavent,Tristan Cragnolini,Anna Caroline E Dahl,Samuela Pasqualiet al. Bioinformatics, 2015, 31 (9), pp.1478-1480. ⟨10.1093/bioinformatics/btu822⟩ Article dans une revue hal-01230764v1
Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion Tyler Reddy,David Shorthouse,Daniel L Parton,Elizabeth Jefferys,Philip W Fowleret al. Structure, 2015, 23 (3), pp.584-97. ⟨10.1016/j.str.2014.12.019⟩ Article dans une revue hal-01230763v1
Predicting and exploring complex nucleic acids architectures through a coarse-grained model T. Cragnolini,S. Doutreligne,Marc Baaden,Philippe Derreumaux,S. Pasquali Journal of Biomolecular Structure and Dynamics, 2015, 33, pp.30--31. ⟨10.1080/07391102.2015.1032593⟩ Article dans une revue hal-01498028v1
Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Gustavo Moraga-Cid,Ludovic Sauguet,Christèle Huon,Laurie Malherbe,Christine Girard-Blancet al. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (9), pp.2865-70. ⟨10.1073/pnas.1417864112⟩ Article dans une revue hal-01230762v1
Taming molecular flexibility to tackle rare diseases. Maria Vittoria Cubellis,Marc Baaden,Giuseppina Andreotti Biochimie, 2015, 113, pp.54-8. ⟨10.1016/j.biochi.2015.03.018⟩ Article dans une revue hal-01230761v1
Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software. Serge Pérez,Thibault Tubiana,Anne Imberty,Marc Baaden Glycobiology, 2015, 25 (5), pp.483-91. ⟨10.1093/glycob/cwu133⟩ Article dans une revue hal-01230766v1
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Fabio Sterpone,Simone Melchionna,Pierre Tuffery,Samuela Pasquali,Normand Mousseauet al. Chemical Society Reviews, 2014, pp.4871-4893. ⟨10.1039/C4CS00048J⟩ Article dans une revue hal-01084631v1
Molecular simulations and visualization: introduction and overview. Jonathan D Hirst,David R Glowacki,Marc Baaden Faraday Discussions, 2014, 169, pp.9-22. ⟨10.1039/c4fd90024c⟩ Article dans une revue hal-01084628v1
Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly Anne-Elisabeth Molza,Nicolas Férey,Mirjam Czjzek,Elisabeth Le Rumeur,Jean-François Hubertet al. Faraday Discussions, 2014, 169, pp.45-62. ⟨10.1039/C3FD00134B⟩ Article dans une revue hal-01018071v1
ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations Matthieu Dreher,Jessica Prevoteau-Jonquet,Mikael Trellet,Marc Piuzzi,Marc Baadenet al. Faraday Discussions, 2014, Molecular simulations and visualization, 169, pp.119-142. ⟨10.1039/C3FD00142C⟩ Article dans une revue hal-00942627v1
Multiscale Simulations Give Insight into the Hydrogen in- and out-Pathways of [NiFe]-Hydrogenases from Aquifex Aeolicus and Desulfovibrio Fructosovorans. Francesco Oteri,Marc Baaden,Elisabeth Lojou,Sophie Sacquin-Mora Journal of Physical Chemistry B, 2014, 118 (48), pp.13800-13811. ⟨10.1021/jp5089965⟩ Article dans une revue hal-01084622v1
A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450. Mian Wang,Marc Baaden,Jianyi Wang,Zhiqun Liang Journal of Chemical Information and Modeling, 2014, pp.1218-25. ⟨10.1021/ci400660e⟩ Article dans une revue hal-01084632v1
The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes Francesco Oteri,Alexandre Ciaccafava,Anne De Poulpiquet,Marc Baaden,Elisabeth. Lojouet al. Physical Chemistry Chemical Physics, 2014, 16 (23), pp.11318-11322. ⟨10.1039/C4CP00510D⟩ Article dans une revue hal-01493492v1
MANHaptic: A Haptic Adaptive Method for Precise Manipulation, Assembly and Navigation A. Tek,Marc Baaden,N. Férey,P. Bourdot International Journal on Human Machine Interaction, 2014, 1, pp.57-63 Article dans une revue hal-01498081v1
Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Ludovic Sauguet,Frédéric Poitevin,Samuel Murail,Catherine van Renterghem,Gustavo Moraga-Cidet al. EMBO Journal, 2013, 32 (5), pp.728-41. ⟨10.1038/emboj.2013.17⟩ Article dans une revue hal-01084646v1
Understanding small biomolecule-biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. Dominique Costa,Pierre-Alain Garrain,Marc Baaden Journal of Biomedical Materials Research Part A, 2013, 101A (4), pp.1210-1222. ⟨10.1002/jbm.a.34416⟩ Article dans une revue istex hal-00760127v1
Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallography Marc Baaden,Marc Delarue ESRF Highlights, 2013, pp.44-45 Article dans une revue (article de synthèse) hal-01498088v1
Interactive Molecular Dynamics: Scaling up to Large Systems Matthieu Dreher,Marc Piuzzi,Ahmed Turki,Matthieu Chavent,Marc Baadenet al. Procedia Computer Science, 2013, 2013 International Conference on Computational Science, 18, pp.20-29. ⟨10.1016/j.procs.2013.05.165⟩ Article dans une revue hal-01084652v1
Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. Daniel L Parton,Alex Tek,Marc Baaden,Mark S P Sansom PLoS Computational Biology, 2013, 9 (4), pp.e1003034. ⟨10.1371/journal.pcbi.1003034⟩ Article dans une revue hal-01084643v1
Coarse-grain modelling of protein-protein interactions. Marc Baaden,Siewert J Marrink Current Opinion in Structural Biology, 2013, 23 (6), pp.878-86. ⟨10.1016/j.sbi.2013.09.004⟩ Article dans une revue hal-01084639v1
Game on, science - how video game technology may help biologists tackle visualization challenges. Zhihan Lv,Alex Tek,Franck da Silva,Charly Empereur-Mot,Matthieu Chaventet al. PLoS ONE, 2013, 8 (3), pp.e57990. ⟨10.1371/journal.pone.0057990⟩ Article dans une revue hal-01084644v1
Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk Leonardo Darré,Alex Tek,Marc Baaden,Sergio Pantano Journal of Chemical Theory and Computation, 2012, 8 (10), pp.3880-3894. ⟨10.1021/ct3001816⟩ Article dans une revue hal-00760151v1
A locally closed conformation of a bacterial pentameric proton-gated ion channel. Marie S Prevost,Ludovic Sauguet,Hugues Nury,Catherine van Renterghem,Christèle Huonet al. Nature Structural and Molecular Biology, 2012, 19 (6), pp.642-9. ⟨10.1038/nsmb.2307⟩ Article dans une revue istex hal-00760125v1
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 Matthieu Chavent,Marc Baaden,Éric Hénon,Serge Antonczak L'Actualité Chimique, 2012, 363, pp.42-46 Article dans une revue hal-00760143v1
GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids. Matthieu Chavent,Antoine Vanel,Alex Tek,Bruno Levy,Sophie Robertet al. Journal of Computational Chemistry, 2011, 32 (13), pp.2924-35. ⟨10.1002/jcc.21861⟩ Article dans une revue hal-00645162v1
Enzyme closure and nucleotide binding structurally lock guanylate kinase. Olivier Delalande,Sophie Sacquin-Mora,Marc Baaden Biophysical Journal, 2011, 101 (6), pp.1440-9. ⟨10.1016/j.bpj.2011.07.048⟩ Article dans une revue hal-00645163v1
GPU-powered tools boost molecular visualization. Matthieu Chavent,Bruno Lévy,Michael Krone,Katrin Bidmon,Jean-Philippe Nominéet al. Briefings in Bioinformatics, 2011, 12 (6), pp.689-701. ⟨10.1093/bib/bbq089⟩ Article dans une revue hal-00645161v1
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. Laurent J Catoire,Marjorie Damian,Marc Baaden,Eric Guittet,Jean-Louis Banères Journal of Biomolecular NMR, 2011, 50 (3), pp.191-195. ⟨10.1007/s10858-011-9523-3⟩ Article dans une revue istex hal-03011659v1
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Hugues Nury,Catherine van Renterghem,Yun Weng,Alphonso Tran,Marc Baadenet al. Nature, 2011, 469 (7330), pp.428-31. ⟨10.1038/nature09647⟩ Article dans une revue hal-00645160v1
One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue Hugues Nury,Frédéric Poitevin,Catherine van Renterghem,Jean-Pierre Changeux,Pierre-Jean Corringeret al. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (14), pp.6275-6280. ⟨10.1073/pnas.1001832107⟩ Article dans une revue pasteur-02174737v1
Photocontrol of Protein Activity in Cultured Cells and Zebrafish with One- and Two-Photon Illumination Deepak Kumar Sinha,Pierre Neveu,Nathalie Gagey,Isabelle Aujard,Chouaha Benbrahim-Bouzidiet al. ChemBioChem, 2010, 11 (5), pp.653-663. ⟨10.1002/cbic.201000008⟩ Article dans une revue hal-03904748v1
General discussion Marc Baaden Faraday Discussions, 2010, 144, pp.203-222. ⟨10.1039/B917708F⟩ Article dans une revue istex hal-03904767v1
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Adrien Saladin,Christopher Amourda,Pierre Poulain,Nicolas Férey,Marc Baadenet al. Nucleic Acids Research, 2010, 38 (19), pp.6313-23. ⟨10.1093/nar/gkq459⟩ Article dans une revue hal-00533099v1
Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues Pierre-Jean Corringer,Marc Baaden,Nicolas Bocquet,Marc Delarue,Virginie Dufresneet al. The Journal of Physiology, 2010, 588 (4), pp.565-572. ⟨10.1113/jphysiol.2009.183160⟩ Article dans une revue pasteur-02174745v1
The Molecular Recognition Mechanism for Superoxide Dismutase Presequence Binding to the Mitochondrial Protein Import Receptor Tom20 from Oryza sativa Involves an LRTLA Motif Yubo Zhang,Marc Baaden,Junjie Yan,Jinzhen Shao,Su Qiuet al. Journal of Physical Chemistry B, 2010, 114 (43), pp.13839-13846. ⟨10.1021/jp103547s⟩ Article dans une revue hal-03904752v1
How cations can assist DNase I in DNA binding and hydrolysis. Marc Guéroult,Daniel Picot,Joséphine Abi-Ghanem,Brigitte Hartmann,Marc Baaden PLoS Computational Biology, 2010, 6 (11), pp.e1001000. ⟨10.1371/journal.pcbi.1001000⟩ Article dans une revue hal-00645165v1
Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Olivier Delalande,Nicolas Ferey,Benoist Laurent,Marc Gueroult,Brigitte Hartmannet al. Pacific Symposium on Biocomputing, 2010, pp.205-15. ⟨10.1142/9789814295291_0023⟩ Article dans une revue hal-00661430v1
Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress Sophie Sacquin-Mora,Olivier Delalande,Marc Baaden Biophysical Journal, 2010, 99 (10), pp.3412-3419. ⟨10.1016/j.bpj.2010.09.026⟩ Article dans une revue hal-00602505v1
General discussion Marc Baaden Faraday Discussions, 2010, 144, pp.445-466. ⟨10.1039/B917710H⟩ Article dans une revue istex hal-03904769v1
Complex molecular assemblies at hand via interactive simulations. Olivier Delalande,Nicolas Férey,Gilles Grasseau,Marc Baaden Journal of Computational Chemistry, 2009, 30 (15), pp.2375-87. ⟨10.1002/jcc.21235⟩ Article dans une revue istex inserm-00713313v1
X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation Nicolas Bocquet,Hugues Nury,Marc Baaden,Chantal Le Poupon,Jean-Pierre Changeuxet al. Nature, 2009, 457 (7225), pp.111-114. ⟨10.1038/nature07462⟩ Article dans une revue istex pasteur-02175132v1
Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States Marie-Pierre Durrieu,Peter Bond,Mark Sansom,Richard Lavery,Marc Baaden ChemPhysChem, 2009, 10 (9-10), pp.1548-1552. ⟨10.1002/cphc.200900216⟩ Article dans une revue hal-03904871v1
Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers Katherine Cox,Peter Bond,Alessandro Grottesi,Marc Baaden,Mark Sansom European Biophysics Journal, 2008, 37 (2), pp.131-141. ⟨10.1007/s00249-007-0185-8⟩ Article dans une revue istex hal-03904877v1
Microseconds Dynamics Simulations of the Outer-Membrane Protease T Marilisa Neri,Marc Baaden,Vincenzo Carnevale,Claudio Anselmi,Amos Maritanet al. Biophysical Journal, 2008, 94 (1), pp.71-78. ⟨10.1529/biophysj.107.116301⟩ Article dans une revue hal-03904879v1
Interactions between neuronal fusion proteins explored by molecular dynamics. Mp Durrieu,R. Lavery,Marc Baaden Biophysical Journal, 2008, 94 (9), pp.3436-3446. ⟨10.1529/biophysj.107.123117⟩ Article dans une revue hal-00315180v1
Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database Kaihsu Tai,Marc Baaden,Stuart Murdock,Bing Wu,Muan Hong Nget al. Journal of Molecular Graphics and Modelling, 2007, 25 (6), pp.896-902. ⟨10.1016/j.jmgm.2006.08.010⟩ Article dans une revue hal-03905209v1
Membrane protein structure quality in molecular dynamics simulation Richard Law,Charlotte Capener,Marc Baaden,Peter Bond,Jeff Campbellet al. Journal of Molecular Graphics and Modelling, 2005, 24 (2), pp.157-165. ⟨10.1016/j.jmgm.2005.05.006⟩ Article dans une revue istex hal-03907341v1
Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations José Faraldo-Gómez,Lucy Forrest,Marc Baaden,Peter Bond,Carmen Domeneet al. Proteins - Structure, Function and Bioinformatics, 2004, 57 (4), pp.783-791. ⟨10.1002/prot.20257⟩ Article dans une revue istex hal-03907343v1
OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme Marc Baaden,Mark S.P. Sansom Biophysical Journal, 2004, 87 (5), pp.2942-2953. ⟨10.1529/biophysj.104.046987⟩ Article dans une revue hal-03907344v1
Theoretical Studies on Lanthanide Cation Extraction by Picolinamides: Ligand–Cation Interactions and Interfacial Behavior Marc Baaden,Frédéric Berny,Charles Madic,Rachel Schurhammer,Georges Wipff Solvent Extraction and Ion Exchange, 2003, 21 (2), pp.199-220. ⟨10.1081/SEI-120018946⟩ Article dans une revue hal-02951773v1
Extending the Structure of an ABC Transporter to Atomic Resolution: Modeling and Simulation Studies of MsbA Jeff Campbell,Philip Biggin,Marc Baaden,Mark Sansom Biochemistry, 2003, 42 (13), pp.3666-3673. ⟨10.1021/bi027337t⟩ Article dans une revue istex hal-03911326v1
A Molecular Dynamics Investigation of Mono and Dimeric States of the Outer Membrane Enzyme OMPLA Marc Baaden,Christoph Meier,Mark Sansom,Mark S.P. Sansom Journal of Molecular Biology, 2003, 331 (1), pp.177-189. ⟨10.1016/s0022-2836(03)00718-6⟩ Article dans une revue istex hal-03911449v1
Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/&quot;oil&quot;/TBP solutions with a comparison of supercritical CO2 and chloroform Marc Baaden,Rachel Schurhammer,Georges Wipff Journal of Physical Chemistry B, 2002, 106 (2), pp.434-441. ⟨10.1021/jp0123785⟩ Article dans une revue istex hal-03165795v1
TBP at the Water−Oil Interface: The Effect of TBP Concentration and Water Acidity Investigated by Molecular Dynamics Simulations Marc Baaden,M. Burgard,G. Wipff Journal of Physical Chemistry B, 2001, 105 (45), pp.11131-11141. ⟨10.1021/jp011890n⟩ Article dans une revue istex hal-03911461v1
Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations Marc Baaden,Michel Burgard,Christian Boehme,Georges Wipff Physical Chemistry Chemical Physics, 2001, 3 (7), pp.1317-1325. ⟨10.1039/B009859K⟩ Article dans une revue hal-03911468v1
The chloroform / TBP / aqueous nitric acid interfacial system: a molecular dynamics investigation Marc Baaden,F. Berny,G. Wipff Journal of Molecular Liquids, 2001, 90 (1-3), pp.1-9. ⟨10.1016/S0167-7322(00)00174-4⟩ Article dans une revue istex hal-03911463v1
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 Marc Baaden,Georges Wipff,Mohamed Reza Yaftian,Michel Burgard,Dominique Matt Journal of the Chemical Society, Perkin Transactions 2, 2000, 7, pp.1315-1322. ⟨10.1039/B000019L⟩ Article dans une revue hal-03920024v1
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 Marc Baaden,P. Granger,A. Strich Molecular Physics, 2000, 98 (6), pp.329-342. ⟨10.1080/00268970009483297⟩ Article dans une revue hal-03920108v1
Calix[4]arenes as Selective Extracting Agents. An NMR Dynamic and Conformational Investigation of the Lanthanide(III) and Thorium(IV) Complexes Bernard Lambert,Vincent Jacques,Alexander Shivanyuk,Susan Matthews,Abdi Tunayaret al. Inorganic Chemistry, 2000, 39 (10), pp.2033-2041. ⟨10.1021/ic990683n⟩ Article dans une revue istex hal-03920094v1
M 3+ Lanthanide Cation Solvation by Acetonitrile: The Role of Cation Size, Counterions, and Polarization Effects Investigated by Molecular Dynamics and Quantum Mechanical Simulations Marc Baaden,F. Berny,C. Madic,G. Wipff Journal of Physical Chemistry A, 2000, 104 (32), pp.7659-7671. ⟨10.1021/jp001352v⟩ Article dans une revue istex hal-03920006v1
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 L. Troxler,Marc Baaden,V. Böhmer,G. Wipff Supramolecular Chemistry, 2000, 12 (1), pp.27-51. ⟨10.1080/10610270008029803⟩ Article dans une revue hal-03919995v1
Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study Marc Baaden,Frédéric Berny,Christian Boehme,Nicolas Muzet,Rachel Schurhammeret al. Journal of Alloys and Compounds, 2000, 303, pp.104-111. ⟨10.1016/S0925-8388(00)00657-5⟩ Article dans une revue hal-02956544v1

Communication dans un congrès (25)

Molecular Modeling of NOX5 protein: Impact of the Initial Structure and Membrane composition Baptiste Etcheverry,Aurélien de la Lande,Marc Baaden,Fabien Cailliez Rencontres ThéMoSiA – RCTF2024, Jun 2024, Rouen (FR), France Communication dans un congrès hal-05368664v1
Escape from PharmaZ: a Game to Boost Pharmacophore Learning through Immersive Augmented Reality Iza Marfisi-Schottman,Hubert Santuz,Camille Bisson,Marc Baaden,Nicolas Féreyet al. Games and Learning Alliance 13th International Conference, GALA 2024, Nov 2024, Berlin, Germany. pp.317-327, ⟨10.1007/978-3-031-78269-5_30⟩ Communication dans un congrès hal-04794554v1
UnityMol-Lite: Cross-platform Collaboration and Interactive Methods for Molecular Modeling in XR Mariano Spivak,Bastien Vincke,Hubert Santuz,Jérôme Hénin,Antoine Talyet al. EuroXR 2024: Proceedings of the 21st EuroXR International Conference, Patrick Bourdot; Mónica González; Jerome Perret; Gabriel Zachmann; Arcadio Reyes-Lecuona, Nov 2024, Athens, Greece Communication dans un congrès hal-05163459v1
GazeMolVR: Sharing Eye-Gaze Cues in a Collaborative VR Environment for Molecular Visualization Rajkumar Darbar,Hubert Santuz,Antoine Taly,Marc Baaden International Conference on Mobile and Ubiquitous Multimedia (MUM '24), December 1--4, 2024, Stockholm, Sweden, Dec 2024, Stockholm (Suède), Sweden. ⟨10.1145/3701571.3701599⟩ Communication dans un congrès hal-04794567v1
Molecular Modeling of NOX5 protein: Impact of the Initial Structure and Membrane composition Baptiste Etcheverry,Aurélien de la Lande,Marc Baaden,Fabien Cailliez NOX-ROS 2023, Nov 2023, Orsay, France Communication dans un congrès hal-05368680v1
Simulation moléculaire du transfert d’électron transmembranaire dans NOX5 F. Cailliez,Xiaojing Wu,Jérôme Hénin,Laura Baciou,Marc Baadenet al. 3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France Communication dans un congrès hal-04426169v1
QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces Xavier Martinez,Michael Krone,Marc Baaden MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2019, Jun 2019, Porto, Portugal. ⟨10.2312/molva.20191095⟩ Communication dans un congrès hal-02370900v1
Molecular Visualization of Computational Biology Data: A Survey of Surveys Naif Alharbi,Mohammed Alharbi,Xavier Martinez,Michael Krone,Alexander S. Roseet al. EuroVis 2017 - Short Papers, Jun 2017, Barcelone, Spain. ⟨10.2312/eurovisshort.20171146⟩ Communication dans un congrès hal-01644549v1
Interactive Visual Analytics of Molecular Data in Immersive Environments via a Semantic Definition of the Content and the Context Mikael Trellet,Nicolas Férey,Marc Baaden,Patrick Bourdot IEEE VR 2016/VR 2016 Workshop on Immersive Analytics, Mar 2016, Greenville, SC, United States. pp.48-53, ⟨10.1109/IMMERSIVE.2016.7932383⟩ Communication dans un congrès hal-01497990v1
Content and task based navigation for structural biology in 3D environments M. Trellet,N. Ferey,Marc Baaden,P. Bourdot 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⟩ Communication dans un congrès hal-01498020v1
UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules S. Doutreligne,C. Gageat,T. Cragnolini,A. Taly,S. Pasqualiet al. 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⟩ Communication dans un congrès hal-01498023v1
UnityMol: Interactive scientific visualization for integrative biology S. Doutreligne,T. Cragnolini,S. Pasquali,P. Derreumaux,Marc Baaden IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV) 2014, 2014, Paris, France. pp.109--110 Communication dans un congrès hal-01498055v1
Content-guided Navigation in Multimeric Molecular Complexes M. Trellet,Nicolas Férey,M. Baaden,P. Bourdot 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⟩ Communication dans un congrès hal-01498053v1
Navigation guidée par le contenu pour l'exploration moléculaire. M. Trellet,N. Férey,M. Baaden,P. Bourdot Journées de l’Association Française de Réalité Virtuelle (AFRV), 2013, Laval, France Communication dans un congrès hal-01498083v1
Molecular Modeling of Hydrogenase Enzymes for Biofuel Cell Design Francesco Oteri,Anne de Poulpiquet,Alexandre Ciaccafava,Elisabeth Lojou,Marc Baaden 57th Annual Meeting of the Biophysical-Society, Feb 2013, Philadelphia, United States. pp.335a, ⟨10.1016/j.bpj.2012.11.1864⟩ Communication dans un congrès hal-03079239v1
Interactive Molecular Dynamics: Scaling up to Large Systems Matthieu Dreher,Marc Piuzzi,Turki Ahmed,Chavent Matthieu,Marc Baadenet al. International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain Communication dans un congrès hal-00809024v1
BioSpring: an interactive and multi-resolution software for flexible docking and for mechanical exploration of large biomolecular assemblies Nicolas Ferey,Olivier Delalande,Marc Baaden JOBIM 2012 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.433-434 Communication dans un congrès hal-00761683v1
FvNano: A Virtual Laboratory to Manipulate Molecular Systems Matthieu Chavent,Marc Piuzzi,Alex Tek,Marc Baaden 1st IEEE symposium on biological data visualization, @ ieee visweek, 2011, Oct 2011, Providence, RI, United States. pp.136 Communication dans un congrès hal-01498124v1
Illustration moléculaire en Chimie et Biologie : exemples, état de l’art et perspectives Marc Baaden Du réel à l'image, Congrès de l’AEIMS, Nov 2011, Strasbourg, France. pp.74-78 Communication dans un congrès hal-03948334v1
Molecular Illustration in Chemistry and Biology: examples, state-of-art and outlook Marc Baaden Reality Through Image, AEIMS Congress, Nov 2011, Strasbourg, France. pp.74-78 Communication dans un congrès hal-03948350v1
A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors Matthieu Chavent,Antoine Vanel,Alex Teck,Bruno Levy,Bruno Raffinet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), 2010, Unknown, France Communication dans un congrès hal-00953423v1
A VR framework for interacting with molecular simulations Nicolas Férey,Olivier Delalande,Gilles Grasseau,Marc Baaden the 2008 ACM symposium, Oct 2008, Bordeaux, France. pp.91-94, ⟨10.1145/1450579.1450598⟩ Communication dans un congrès hal-03904892v1
From Interactive to Immersive Molecular Dynamics Nicolas Férey,Olivier Delalande,Gilles Grasseau,Marc Baaden Workshop in Virtual Reality Interactions and Physical Simulation "VRIPHYS" (2008), 2008, Grenoble, France. pp.89-96, ⟨10.2312/PE/vriphys/vriphys08/089-096⟩ Communication dans un congrès hal-03904907v1
Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex: a Grand Challenge Project on the DEISA HPC Infrastructure Elmar Krieger,Laurent Leger,Marie-Pierre Durrieu,Nada Taib,Peter Bondet al. Parallel Computing: Architectures, Algorithms and Applications, Sep 2007, Julich, Germany. pp.729-736 Communication dans un congrès hal-03907311v1
Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores Marc Baaden,F. Berny,N. Muzet,R. Schurhammer,Laurent Troxleret al. 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 Communication dans un congrès hal-03920295v1

Poster de conférence (6)

Between two walls: Modeling the adsorption behavior of redox enzymes on bare and SAM-functionalised gold surfaces Sophie Sacquin-Mora,Nicolas Bourassin,Florent Barbault,Marc Baaden XXIIIème congrès du GGMM, May 2023, Toulouse, France Poster de conférence hal-04112652v1
Structure-Function analysis of the yeast mitofusin Fzo1 Laetitia Cavellini,Maria de los Ángeles Morcillo Parra,Antoine Taly,Marc Baaden,Mickael M. Cohen 22ème congrès du Groupe Français de Bioenergetique, Sep 2023, Bedoin, France Poster de conférence hal-04466677v1
Molecular Modeling of NOX5 protein: Impact of the Initial Structure and Membrane composition Baptiste Etcheverry,Aurélien de la Lande,Marc Baaden,Fabien Cailliez GGMM 2023, May 2023, Toulouse, France Poster de conférence hal-05368690v1
Etude dynamique théorique de la structure de NOX5 Baptiste Etcheverry,Fabien Cailliez,Aurélien de la Lande,Marc Baaden 3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (FR), France Poster de conférence hal-05368696v1
Modeling enzymes interacting with functionalized surfaces: lessons from multiscale modeling approaches Nicolas Bourassin,Florent Barbault,Marc Baaden,Sophie Sacquin-Mora 66th Biophysical Society Annual Meeting, 2022, San Francisco, United States. Biophysical Journal, 121 (3), pp.135a, 2022, ⟨10.1016/j.bpj.2021.11.2057⟩ Poster de conférence hal-05591793v1
A Multimodal VR Framework for Interactive Molecular Simulations Alex Tek,Benoist Laurent,Nicolas Férey,Marc Baaden EuroVR-EVE 2010, Nov 2010, Orsay, France Poster de conférence hal-03977463v1

Proceedings/Recueil des communications (4)

Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK Mihail Barboiu,Manish Kumar,Marc Baaden,Philip Gale,Bruce Hinds Chemical Communications, 55 (27), pp.3853-3858, 2019, ⟨10.1039/c9cc90112d⟩ Proceedings/Recueil des communications hal-02127512v1
Visualization of Biomolecular Structures: State of the Art Barbora Kozlíková,Michael Krone,Norbert Lindow,Martin Falk,Marc Baadenet al. EuroVisSTAR2015, The Eurographics Association, 2015, Eurographics Conference on Visualization (EuroVis) - STARs, ⟨10.2312/eurovisstar.20151112⟩ Proceedings/Recueil des communications hal-03902339v1
Modeling complex biological systems: From solution chemistry to membranes and channels Benoist Laurent,Samuel Murail,Franck da Silva,Pierre-Jean Corringer,Marc Baaden Pure and Applied Chemistry, 85 (1), pp.1-13, 2013, ⟨10.1351/PAC-CON-12-04-10⟩ Proceedings/Recueil des communications hal-00760163v1
La réalité virtuelle au laboratoire de Biochimie Théorique - toucher, déformer et assembler des molécules du bout des doigts Marc Baaden Journal de l'AFRV, 10, pp.4-5, 2011 Proceedings/Recueil des communications hal-03948409v1

Ouvrages (1)

Itinéraires Bis Axel Kahn,Sebastien Fleuret,Sébastien Descotes-Genon,Nicolas B. Garnier,Carole Leveneset al. 2009, Connaissance et savoirs, 978-2-7539-0164-3 Ouvrages halshs-02424173v1

Chapitre d'ouvrage (13)

5. Les supercalculateurs et l'intelligence artificielle révèlent le monde moléculaire Marc Baaden,Fabio Sterpone,Antoine Taly Le calcul pour les Big Data et l’Intelligence Artificielle, pp.138-141, A paraître Chapitre d'ouvrage hal-04799896v1
Interactive Molecular Dynamics André Lanrezac,Nicolas Férey,Marc Baaden Comprehensive Computational Chemistry, 3, Elsevier, pp.454-474, 2024, ⟨10.1016/B978-0-12-821978-2.00115-X⟩ Chapitre d'ouvrage hal-04307111v1
Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers A Hardiagon,S Murail,L Huang,M Barboiu,F Sterponeet al. 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⟩ Chapitre d'ouvrage hal-02944940v1
Voir et manipuler les molécules. Du virtuel au réel Marc Baaden,Emmanuel Maisonhaute 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 Chapitre d'ouvrage hal-03211883v1
Computer Simulations Provide Guidance for Molecular Medicine through Insights on Dynamics and Mechanisms at the Atomic Scale Marc Baaden 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⟩ Chapitre d'ouvrage hal-02370021v1
Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels Xavier Martinez,Arthur Hardiagon,Hubert Santuz,Samuel Murail,Mihail Barboiuet al. 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⟩ Chapitre d'ouvrage hal-02944941v1
The modelling and enhancement of water hydrodynamics: general discussion Marc Baaden,Manash Pratim Borthakur,Serena Casanova,Rob Coalson,Viatcheslav Fregeret al. Faraday Discussions, 209, pp.273-285, 2018, ⟨10.1039/C8FD90021C⟩ Chapitre d'ouvrage hal-02370038v1
Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins Jérôme Hénin,Marc Baaden,Antoine Taly 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⟩ Chapitre d'ouvrage hal-01498051v1
Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations Alex Tek,Benoist Laurent,Marc Piuzzi,Zhihan Lu,Matthieu Chaventet al. 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⟩ Chapitre d'ouvrage hal-00760181v1
Physicochimie : molécules, milieux Philippe Hapiot,Mustapha Abdelmoula,Xavier Assfeld,Jean Aupiais,Marc Baadenet al. RAPPORT DE CONJONCTURE 2010 du Comité national de la recherche scientifique, CNRS Editions, pp.243-263, 2010, 978-2-271-07263-4 Chapitre d'ouvrage hal-03977638v1
Chapter 9. Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels Syma Khalid,Marc Baaden Molecular Simulations and Biomembranes, Royal Society of Chemistry, pp.225-247, 2010, RSC Biomolecular Sciences, ⟨10.1039/9781849732154-00225⟩ Chapitre d'ouvrage istex hal-03904759v1
There's plenty of room in the middle: Multiscale Modelling of Biological Systems Marc Baaden,Richard Lavery Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Singpost, pp.173-196, 2007, 978-81-309-0208-4 Chapitre d'ouvrage hal-03907310v1
Interfacial Features of Assisted Liquid-Liquid Extraction of Uranyl and Cesium Salts: A Molecular Dynamics Investigation Marc Baaden,F. Berny,N. Muzet,L. Troxler,G. Wipff Calixarenes for Separations, 757, American Chemical Society, pp.71-85, 2000, ACS Symposium Series, ⟨10.1021/bk-2000-0757.ch006⟩ Chapitre d'ouvrage hal-03920161v1

Autre publication scientifique (4)

Vitamins : Visual and In Situ Analytics for Molecular Interactive Simulation Marc Baaden,Matthieu Dreher,Nicolas Ferey,Sébastien Limet,Jessica Prevoteau-Jonquetet al. 2014 Autre publication scientifique hal-01313096v1
Visualiser, toucher, déformer et assembler des nano-objets du bout des doigts Marc Baaden Les nanotechnologies : un nouveau paradigme, Les Cahiers de l’ANR - n°5, 2012, pp.47 Autre publication scientifique hal-03948139v2
Toucher, déformer et assembler des molécules du bout des doigts Marc Baaden Le calcul intensif: technologie clé pour le futur, Les Cahiers de l'ANR - n° 3, 2010, pp.71 Autre publication scientifique hal-03977530v1
Molecular Modeling with the ChemOffice Ultra 4.5 Program Suite Marc Baaden 2000 Autre publication scientifique hal-03921142v1

Pré-publication, Document de travail (1)

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study Staëlle Makamte,Amira Jabrani,Annick Paquelin,Anne Plessis,Mathieu Sanialet al. 2023 Pré-publication, Document de travail hal-04019989v1

Thèse (1)

Etudes de molécules extractantes en solution et aux interfaces liquide-liquide : aspects structuraux et mécanistiques des effets de synergie Marc Baaden Autre. Université Louis Pasteur - Strasbourg I, 2003. Français. ⟨NNT : ⟩ Thèse tel-00002812v2

HDR (1)

Simulations numériques de systèmes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes Marc Baaden Sciences pharmaceutiques. Université Paris-Diderot - Paris VII, 2010 HDR tel-00541521v1