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Marc Baaden



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State of the Art of Molecular Visualization in Immersive Virtual Environments

David Kuťák , Pere‐pau Vázquez , Tobias Isenberg , Michael Krone , Marc Baaden
Computer Graphics Forum, 2023, 42 (6), pp.e14738:1--e14738:29. ⟨10.1111/cgf.14738⟩
Journal articles hal-04006531v1
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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⟩
Journal articles hal-04306431v1
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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 , Mihail Barboiu
Journal of the American Chemical Society, 2023, 145 (40), pp.21904-21914. ⟨10.1021/jacs.3c06335⟩
Journal articles hal-04257737v1
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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 Ogoshi
Angewandte Chemie International Edition, 2023, 62 (42), pp.e202310812. ⟨10.1002/anie.202310812⟩
Journal articles hal-04257786v1
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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⟩
Journal articles hal-04306427v1
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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⟩
Journal articles hal-04257762v1
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Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT

Yubo Zhang , Marc Baaden
Catalysts, 2023, 13 (2), pp.214. ⟨10.3390/catal13020214⟩
Journal articles hal-03943290v1
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A Perspective on the pospective use of AI in protein structure prediction

Raphaelle Versini , Sujith Sritharan , Burcu Aykaç Fas , Thibault Tubiana , Sana Zineb Aimeur
Journal of Chemical Information and Modeling, 2023, 64 (1), pp.26-41. ⟨10.1021/acs.jcim.3c01361⟩
Journal articles hal-04306436v1
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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⟩
Journal articles hal-03873715v1
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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⟩
Journal articles hal-03294641v1
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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⟩
Journal articles hal-03873706v1
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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⟩
Journal articles hal-03873725v1
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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⟩
Journal articles hal-03873710v1
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Design – a new way to look at old molecules

Davide Spalvieri , Anne-Marine Mauviel , Matthieu Lambert , Nicolas Férey , Sophie Sacquin-Mora
Journal of Integrative Bioinformatics, 2022, 19 (2), pp.20220020. ⟨10.1515/jib-2022-0020⟩
Journal articles hal-03793308v1
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Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies

Anne-Elisabeth Molza , Yvonne Westermaier , Magali Moutte , Pierre Ducrot , Claudia Danilowicz
Frontiers in Molecular Biosciences, 2022, 9, pp.826136. ⟨10.3389/fmolb.2022.826136⟩
Journal articles hal-03826944v1
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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 Plessis
Journal of Structural Biology, 2022, 214 (2), pp.107853. ⟨10.1016/j.jsb.2022.107853⟩
Journal articles hal-03413156v1
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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⟩
Journal articles hal-03447181v1
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Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations

Xiaojing Wu , Jérôme Hénin , Laura Baciou , Marc Baaden , Fabien Cailliez
Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩
Journal articles hal-03382660v1
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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⟩
Journal articles hal-02944943v2
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Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic

Núria López , Luigi del Debbio , Marc Baaden , Matej Praprotnik , Laura Grigori
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (46), pp.e2024891118. ⟨10.1073/pnas.2024891118⟩
Journal articles hal-03438495v1
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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⟩
Journal articles hal-03438490v1
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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 Sterpone
Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩
Journal articles hal-03410227v1
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Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation

Li-Bo Huang , Arthur Hardiagon , Istvan Kocsis , Cristina-Alexandra Jegu , Mihai Deleanu
Journal of the American Chemical Society, 2021, 143 (11), pp.4224-4233. ⟨10.1021/jacs.0c11952⟩
Journal articles hal-03364954v2
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Visualizing protein structures - tools and trends

Xavier Martinez , Matthieu Chavent , Marc Baaden
Biochemical Society Transactions, 2020, 48 (2), pp.499-506. ⟨10.1042/BST20190621⟩
Journal articles hal-02946006v1
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Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers

Dmytro Strilets , Shixin Fa , Arthur Hardiagon , Marc Baaden , Tomoki Ogoshi
Angewandte Chemie International Edition, 2020, 59 (51), pp.23213-23219. ⟨10.1002/anie.202009219⟩
Journal articles hal-03028876v1
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Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Joseph Laureanti , Juan Brandi , Elvis Offor , David Engel , Robert Rallo
Protein Science, 2020, 29 (1), pp.237-246. ⟨10.1002/pro.3773⟩
Journal articles hal-02370955v1
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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⟩
Journal articles hal-02939019v1
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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 Baaden
Physical Chemistry Chemical Physics, 2020, 22 (3), pp.1611-1623. ⟨10.1039/C9CP05776E⟩
Journal articles hal-02397135v1
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Scruter les molécules en réalité virtuelle, pour quoi faire ?

Xavier Martinez , Marc Baaden
L'Actualité Chimique, 2020, 448, pp.23-26
Journal articles hal-02946000v1
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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⟩
Journal articles hal-02370047v1
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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⟩
Journal articles hal-02345040v1
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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⟩
Journal articles hal-02345057v1
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Glutathionylation primes soluble GAPDH for late collapse into insoluble aggregates

Mirko Zaffagnini , Christophe H. Marchand , M. Malferrari , Samuel Murail , Sara Bonacchi
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (51), pp.26057-26065. ⟨10.1073/pnas.1914484116⟩
Journal articles hal-02370717v1
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Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

Astrid F. Brandner , Stepan Timr , Simone Melchionna , Philippe Derreumaux , Marc Baaden
Scientific Reports, 2019, 9, pp.16450. ⟨10.1038/s41598-019-52760-y⟩
Journal articles hal-02370975v1
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Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Xavier Martinez , Michael Krone , Naif Alharbi , Alexander Rose , Robert Laramee
Structure, 2019, 27 (11), pp.1617-1623. ⟨10.1016/j.str.2019.09.001⟩
Journal articles hal-02370947v1
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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⟩
Journal articles hal-02345043v1
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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⟩
Journal articles hal-02345034v1
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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 Brito
Journal articles hal-01935588v1
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MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Alexandre Maes , Xavier Martinez , Karen Druart , Benoist Laurent , Sean Guégan
Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180006. ⟨10.1515/jib-2018-0006⟩
Journal articles hal-01935585v1
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Multi-scale simulations of biological systems using the OPEP coarse-grained model

Fabio Sterpone , Sébastien Doutreligne , Thanh Thuy Tran , Simone Melchionna , Marc Baaden
Biochemical and Biophysical Research Communications, 2018, 498 (2), pp.296-304. ⟨10.1016/j.bbrc.2017.08.165⟩
Journal articles hal-01644564v1
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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⟩
Journal articles hal-01883877v1
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Oriented chiral water wires in artificial transmembrane channels

Istvan Kocsis , Mirco Sorci , Heather Vanselous , Samuel Murail , Stephanie Sanders
Science Advances , 2018, 4 (3), pp.eaao5603. ⟨10.1126/sciadv.aao5603⟩
Journal articles hal-01797309v1
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Water permeation across artificial I-quartet membrane channels: from structure to disorder

Samuel Murail , Tudor Vasiliu , Andrei Neamtu , Mihail Barboiu , Fabio Sterpone
Faraday Discussions, 2018, 209, pp.125 - 148. ⟨10.1039/c8fd00046h⟩
Journal articles hal-01926847v1

Biomimetic water channels: general discussion

Marc Baaden , Mihail Barboiu , Roslyn Bill , Chun-Long Chen , Jeffery Davis
Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩
Journal articles hal-01926861v1
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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⟩
Journal articles hal-01935581v1

Applications to water transport systems: general discussion

Marc Baaden , Mihail Barboiu , Manash Pratim Borthakur , Chun-Long Chen , Rob Coalson
Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩
Journal articles hal-01926896v1
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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⟩
Journal articles hal-01935586v1
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Ten simple rules to create a serious game, illustrated with examples from structural biology

Marc Baaden , Olivier Delalande , Nicolas Ferey , Samuela Pasquali , Jérôme Waldispühl
PLoS Computational Biology, 2018, 14 (3), pp.e1005955. ⟨10.1371/journal.pcbi.1005955⟩
Journal articles hal-01744190v1
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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 Pollet
Journal of Biological Chemistry, 2018, 293 (18), pp.6637-6646. ⟨10.1074/jbc.M117.809798⟩
Journal articles hal-01795395v2
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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⟩
Journal articles hal-01935682v1

Structure and function of natural proteins for water transport: general discussion

Marc Baaden , Mihail Barboiu , Roslyn Bill , Serena Casanova , Chun-Long Chen
Faraday Discussions, 2018, 209, pp.83 - 95. ⟨10.1039/C8FD90019A⟩
Journal articles hal-01926768v1
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Controlling Redox Enzyme Orientation at Planar Electrodes

Vivek Pratap Hitaishi , Romain Clément , Nicolas Bourassin , Marc Baaden , Anne de Poulpiquet
Catalysts, 2018, 8 (5), pp.192. ⟨10.3390/catal8050192⟩
Journal articles hal-01793660v1

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⟩
Journal articles hal-01587914v1
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String method solution of the gating pathways for a pentameric ligand-gated ion channel

Bogdan Lev , Samuel Murail , Frédéric Poitevin , Brett A Cromer , Marc Baaden
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (21), pp.E4158 - E4167. ⟨10.1073/pnas.1617567114⟩
Journal articles hal-01644525v1
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Visualization of Biomolecular Structures: State of the Art Revisited

B. Kozlíková , M. Krone , M. Falk , N. Lindow , Marc Baaden
Computer Graphics Forum, 2017, 36 (8), pp.178-204. ⟨10.1111/cgf.13072⟩
Journal articles hal-01400465v1
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A membrane-inserted structural model of the yeast mitofusin Fzo1

Dario de Vecchis , Laetitia Cavellini , Marc Baaden , Jérôme Hénin , Mickaël M. Cohen
Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩
Journal articles hal-01581980v1
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What Can Human-Guided Simulations Bring to RNA Folding?

Liuba Mazzanti , Sébastien Doutreligne , Cédric Gageat , Philippe Derreumaux , Antoine Taly
Biophysical Journal, 2017, 113 (2), pp.302 - 312. ⟨10.1016/j.bpj.2017.05.047⟩
Journal articles hal-01644519v1
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Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation

Erol Licsandru , Istvan Kocsis , Yue-Xiao Shen , Samuel Murail , Yves-Marie Legrand
Journal of the American Chemical Society, 2016, 138 (16), pp.5403 - 5409. ⟨10.1021/jacs.6b01811⟩
Journal articles hal-01400466v1
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Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

Benoist Laurent , Samuel Murail , Azadeh Shahsavar , Ludovic Sauguet , Marc Delarue
Structure, 2016, 24 (4), pp.595 - 605. ⟨10.1016/j.str.2016.02.014⟩
Journal articles hal-01400467v1
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Visual Analysis of Biomolecular Cavities: State of the Art

M. Krone , B. Kozlíková , N. Lindow , Marc Baaden , D. Baum
Computer Graphics Forum, 2016, 35 (3), pp.527 - 551. ⟨10.1111/cgf.12928⟩
Journal articles hal-01400464v1
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Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.

Gustavo Moraga-Cid , Ludovic Sauguet , Christèle Huon , Laurie Malherbe , Christine Girard-Blanc
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (9), pp.2865-70. ⟨10.1073/pnas.1417864112⟩
Journal articles hal-01230762v1

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⟩
Journal articles hal-01498028v1
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Epock : rapid analysis of protein pocket dynamics

Benoist Laurent , Matthieu Chavent , Tristan Cragnolini , Anna Caroline E Dahl , Samuela Pasquali
Bioinformatics, 2015, 31 (9), pp.1478-1480. ⟨10.1093/bioinformatics/btu822⟩
Journal articles hal-01230764v1
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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 Fowler
Structure, 2015, 23 (3), pp.584-97. ⟨10.1016/j.str.2014.12.019⟩
Journal articles hal-01230763v1
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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⟩
Journal articles hal-01230761v1
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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⟩
Journal articles hal-01230766v1

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⟩
Journal articles 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. Lojou
Physical Chemistry Chemical Physics, 2014, 16 (23), pp.11318-11322. ⟨10.1039/C4CP00510D⟩
Journal articles hal-01493492v1
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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 Hubert
Faraday Discussions, 2014, 169, pp.45-62. ⟨10.1039/C3FD00134B⟩
Journal articles hal-01018071v1

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 Mousseau
Chemical Society Reviews, 2014, pp.4871-93. ⟨10.1039/C4CS00048J⟩
Journal articles hal-01084631v1
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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⟩
Journal articles hal-01084628v1
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ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations

Matthieu Dreher , Jessica Prevoteau-Jonquet , Mikael Trellet , Marc Piuzzi , Marc Baaden
Faraday Discussions, 2014, Molecular simulations and visualization, 169, pp.119-142. ⟨10.1039/C3FD00142C⟩
Journal articles hal-00942627v1

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
Journal articles hal-01498081v1

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⟩
Journal articles hal-01084622v1

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
Journal articles hal-01498088v1

Interactive Molecular Dynamics: Scaling up to Large Systems

Matthieu Dreher , Marc Piuzzi , Ahmed Turki , Matthieu Chavent , Marc Baaden
Procedia Computer Science, 2013, 2013 International Conference on Computational Science, 18, pp.20-29. ⟨10.1016/j.procs.2013.05.165⟩
Journal articles 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⟩
Journal articles hal-01084643v1

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.

Ludovic Sauguet , Frédéric Poitevin , Samuel Murail , Catherine van Renterghem , Gustavo Moraga-Cid
EMBO Journal, 2013, 32 (5), pp.728-41. ⟨10.1038/emboj.2013.17⟩
Journal articles 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⟩
Journal articles hal-00760127v1

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/⟩
Journal articles 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 Chavent
PLoS ONE, 2013, 8 (3), pp.e57990. ⟨10.1371/journal.pone.0057990⟩
Journal articles hal-01084644v1

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
Journal articles hal-00760143v1

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⟩
Journal articles 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 Huon
Nature Structural and Molecular Biology, 2012, 19 (6), pp.642-9. ⟨10.1038/nsmb.2307⟩
Journal articles hal-00760125v1

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⟩
Journal articles hal-03011659v1

GPU-powered tools boost molecular visualization.

Matthieu Chavent , Bruno Lévy , Michael Krone , Katrin Bidmon , Jean-Philippe Nominé
Briefings in Bioinformatics, 2011, 12 (6), pp.689-701. ⟨10.1093/bib/bbq089⟩
Journal articles hal-00645161v1

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⟩
Journal articles hal-00645163v1

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 Robert
Journal of Computational Chemistry, 2011, 32 (13), pp.2924-35. ⟨10.1002/jcc.21861⟩
Journal articles hal-00645162v1

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel.

Hugues Nury , Catherine van Renterghem , Yun Weng , Alphonso Tran , Marc Baaden
Nature, 2011, 469 (7330), pp.428-31. ⟨10.1038/nature09647⟩
Journal articles hal-00645160v1

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⟩
Journal articles hal-00602505v1
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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 Hartmann
Pacific Symposium on Biocomputing, 2010, pp.205-15. ⟨10.1142/9789814295291_0023⟩
Journal articles hal-00661430v1
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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-Bouzidi
ChemBioChem, 2010, 11 (5), pp.653-663. ⟨10.1002/cbic.201000008⟩
Journal articles hal-03904748v1

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 Corringer
Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (14), pp.6275-6280. ⟨10.1073/pnas.1001832107⟩
Journal articles pasteur-02174737v1

General discussion

Marc Baaden
Faraday Discussions, 2010, 144, pp.203-222. ⟨10.1039/B917708F⟩
Journal articles hal-03904767v1
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Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.

Adrien Saladin , Christopher Amourda , Pierre Poulain , Nicolas Férey , Marc Baaden
Nucleic Acids Research, 2010, 38 (19), pp.6313-23. ⟨10.1093/nar/gkq459⟩
Journal articles hal-00533099v1

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 Qiu
Journal of Physical Chemistry B, 2010, 114 (43), pp.13839-13846. ⟨10.1021/jp103547s⟩
Journal articles hal-03904752v1
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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 Dufresne
The Journal of Physiology, 2010, 588 (4), pp.565-572. ⟨10.1113/jphysiol.2009.183160⟩
Journal articles pasteur-02174745v1

General discussion

Marc Baaden
Faraday Discussions, 2010, 144, pp.445-466. ⟨10.1039/B917710H⟩
Journal articles hal-03904769v1
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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⟩
Journal articles hal-00645165v1

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 Changeux
Nature, 2009, 457 (7225), pp.111-114. ⟨10.1038/nature07462⟩
Journal articles pasteur-02175132v1

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⟩
Journal articles inserm-00713313v1

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⟩
Journal articles hal-03904871v1

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⟩
Journal articles hal-00315180v1

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⟩
Journal articles hal-03904877v1
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Microseconds Dynamics Simulations of the Outer-Membrane Protease T

Marilisa Neri , Marc Baaden , Vincenzo Carnevale , Claudio Anselmi , Amos Maritan
Biophysical Journal, 2008, 94 (1), pp.71-78. ⟨10.1529/biophysj.107.116301⟩
Journal articles hal-03904879v1

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 Ng
Journal of Molecular Graphics and Modelling, 2007, 25 (6), pp.896-902. ⟨10.1016/j.jmgm.2006.08.010⟩
Journal articles hal-03905209v1

Membrane protein structure quality in molecular dynamics simulation

Richard Law , Charlotte Capener , Marc Baaden , Peter Bond , Jeff Campbell
Journal of Molecular Graphics and Modelling, 2005, 24 (2), pp.157-165. ⟨10.1016/j.jmgm.2005.05.006⟩
Journal articles hal-03907341v1
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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⟩
Journal articles hal-03907344v1

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations

José Faraldo-Gómez , Lucy Forrest , Marc Baaden , Peter Bond , Carmen Domene
Proteins - Structure, Function and Bioinformatics, 2004, 57 (4), pp.783-791. ⟨10.1002/prot.20257⟩
Journal articles hal-03907343v1

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⟩
Journal articles hal-03911326v1

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⟩
Journal articles hal-02951773v1

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⟩
Journal articles hal-03911449v1

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

Marc Baaden , Rachel Schurhammer , Georges Wipff
Journal of Physical Chemistry B, 2002, 106 (2), pp.434-441. ⟨10.1021/jp0123785⟩
Journal articles hal-03165795v1

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⟩
Journal articles hal-03911468v1

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⟩
Journal articles hal-03911461v1

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⟩
Journal articles hal-03911463v1

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⟩
Journal articles hal-03919995v1

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 Tunayar
Inorganic Chemistry, 2000, 39 (10), pp.2033-2041. ⟨10.1021/ic990683n⟩
Journal articles hal-03920094v1

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⟩
Journal articles 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⟩
Journal articles hal-03920108v1
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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 Schurhammer
Journal of Alloys and Compounds, 2000, 303, pp.104-111. ⟨10.1016/S0925-8388(00)00657-5⟩
Journal articles hal-02956544v1

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⟩
Journal articles hal-03920006v1

Simulation moléculaire du transfert d’électron transmembranaire dans NOX5

F. Cailliez , Xiaojing Wu , Jérôme Hénin , Laura Baciou , Marc Baaden
3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France
Conference papers hal-04426169v1
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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⟩
Conference papers hal-02370900v1
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Molecular Visualization of Computational Biology Data: A Survey of Surveys

Naif Alharbi , Mohammed Alharbi , Xavier Martinez , Michael Krone , Alexander S. Rose
EuroVis 2017 - Short Papers, Jun 2017, Barcelone, Spain. ⟨10.2312/eurovisshort.20171146⟩
Conference papers hal-01644549v1
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Interactive Visual Analytics of Molecular Data in Immersive Environments via a Semantic Definition of the Content and the Context

Mickael 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⟩
Conference papers 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⟩
Conference papers hal-01498020v1
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UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules

S. Doutreligne , C. Gageat , T. Cragnolini , A. Taly , S. Pasquali
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⟩
Conference papers hal-01498023v1
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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
Conference papers hal-01498055v1
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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⟩
Conference papers hal-01498053v1
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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
Conference papers 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⟩
Conference papers hal-03079239v1
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Interactive Molecular Dynamics: Scaling up to Large Systems

Matthieu Dreher , Marc Piuzzi , Turki Ahmed , Chavent Matthieu , Marc Baaden
International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain
Conference papers hal-00809024v1
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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
Conference papers hal-00761683v1
Image document

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
Conference papers hal-03948350v1
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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
Conference papers hal-01498124v1
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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
Conference papers hal-03948334v1

A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors

Matthieu Chavent , Antoine Vanel , Alex Teck , Bruno Levy , Bruno Raffin
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), 2010, Unknown, France
Conference papers 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⟩
Conference papers 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⟩
Conference papers hal-03904907v1
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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 Bond
Parallel Computing: Architectures, Algorithms and Applications, Sep 2007, Julich, Germany. pp.729-736
Conference papers hal-03907311v1
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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 Troxler
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
Conference papers hal-03920295v1
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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⟩
Book sections hal-04307111v1

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
Book sections hal-03211883v1
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Stability and structure of adaptive self-organized supramolecular artificial water channels in lipid bilayers

A Hardiagon , S Murail , L Huang , M Barboiu , F Sterpone
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⟩
Book sections hal-02944940v1
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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⟩
Book sections hal-02370021v1
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Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Xavier Martinez , Arthur Hardiagon , Hubert Santuz , Samuel Murail , Mihail Barboiu
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⟩
Book sections hal-02944941v1

The modelling and enhancement of water hydrodynamics: general discussion

Marc Baaden , Manash Pratim Borthakur , Serena Casanova , Rob Coalson , Viatcheslav Freger
Faraday Discussions, 209, pp.273-285, 2018, ⟨10.1039/C8FD90021C⟩
Book sections 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⟩
Book sections hal-01498051v1

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Alex Tek , Benoist Laurent , Marc Piuzzi , Zhihan Lu , Matthieu Chavent
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⟩
Book sections hal-00760181v1

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⟩
Book sections hal-03904759v1

Physicochimie : molécules, milieux

Philippe Hapiot , Mustapha Abdelmoula , Xavier Assfeld , Jean Aupiais , Marc Baaden
RAPPORT DE CONJONCTURE 2010 du Comité national de la recherche scientifique, CNRS Editions, pp.243-263, 2010, 978-2-271-07263-4
Book sections hal-03977638v1
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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
Book sections 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⟩
Book sections hal-03920161v1
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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
Habilitation à diriger des recherches tel-00541521v1