Marc Baaden

189
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Publications

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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
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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 Meuret et al.

Journal of Chemical Theory and Computation, 2025, ⟨10.1021/acs.jctc.5c00688⟩

Article dans une revue hal-05236200v1
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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
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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
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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
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BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics

Benoist Laurent , André Lanrezac , Hubert Santuz , Nicolas Ferey , Olivier Delalande et al.

Protein Science, 2025, 34 (5), pp.e70130. ⟨10.1002/pro.70130⟩

Article dans une revue hal-05039981v1
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A Perspective on the prospective use of AI in protein structure prediction

Raphaelle Versini , Sujith Sritharan , Burcu Aykaç Fas , Thibault Tubiana , Sana Zineb Aimeur et al.

Journal of Chemical Information and Modeling, 2024, 64 (1), pp.26-41. ⟨10.1021/acs.jcim.3c01361⟩

Article dans une revue hal-04306436v1
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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 Lee et al.

Journal of the American Chemical Society, 2024, 147 (1), pp.678-686. ⟨10.1021/jacs.4c13072⟩

Article dans une revue hal-05022271v1
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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
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Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion

Raphaëlle Versini , Marc Baaden , Laetitia Cavellini , Mickaël M Cohen , Antoine Taly et al.

Structure, 2024, 32 (11), pp.1997-2012.e7. ⟨10.1101/2023.09.22.559002⟩

Article dans une revue hal-04299450v1
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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
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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⟩

Article dans une revue hal-03943290v1
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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 , Mihai Barboiu

Journal of the American Chemical Society, 2023, 145 (40), pp.21904-21914. ⟨10.1021/jacs.3c06335⟩

Article dans une revue hal-04257737v1
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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 et al.

Computer Graphics Forum, 2023, 42 (6), pp.e14738:1--e14738:29. ⟨10.1111/cgf.14738⟩

Article dans une revue 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⟩

Article dans une revue hal-04306431v1
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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⟩

Article dans une revue hal-04257762v1
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MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations

Johanna K S Tiemann , Magdalena Szczuka , Lisa Bouarroudj , Mohamed Oussaren , Steven Garcia et al. Article dans une revue hal-04254566v2
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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⟩

Article dans une revue hal-04306427v1
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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 et al.

Angewandte Chemie International Edition, 2023, 62 (42), pp.e202310812. ⟨10.1002/anie.202310812⟩

Article dans une revue hal-04257786v1
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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 et al.

Journal of Structural Biology, 2022, 214 (2), pp.107853. ⟨10.1016/j.jsb.2022.107853⟩

Article dans une revue hal-03413156v1
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Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies

Anne-Elisabeth Molza , Yvonne Westermaier , Magali Moutte , Pierre Ducrot , Claudia Danilowicz et al.

Frontiers in Molecular Biosciences, 2022, 9, pp.826136. ⟨10.3389/fmolb.2022.826136⟩

Article dans une revue hal-03826944v1
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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⟩

Article dans une revue 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⟩

Article dans une revue hal-03873706v1
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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⟩

Article dans une revue hal-03873715v1
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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 et al.

Journal of Integrative Bioinformatics, 2022, 19 (2), pp.20220020. ⟨10.1515/jib-2022-0020⟩

Article dans une revue hal-03793308v1
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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⟩

Article dans une revue hal-03873710v1
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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⟩

Article dans une revue hal-03873725v1
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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 et al.

Frontiers in Chemistry, 2021, 9, ⟨10.3389/fchem.2021.650651⟩

Article dans une revue hal-03382660v1
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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⟩

Article dans une revue hal-03438490v1
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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⟩

Article dans une revue 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 et 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
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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⟩

Article dans une revue hal-03447181v1
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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 et al.

The Journal of Chemical Physics, 2021, 154 (18), pp.184102. ⟨10.1063/5.0044360⟩

Article dans une revue 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 et al.

Journal of the American Chemical Society, 2021, 143 (11), pp.4224-4233. ⟨10.1021/jacs.0c11952⟩

Article dans une revue hal-03364954v2
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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 et al.

Physical Chemistry Chemical Physics, 2020, 22 (3), pp.1611-1623. ⟨10.1039/C9CP05776E⟩

Article dans une revue hal-02397135v1
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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⟩

Article dans une revue 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 et al.

Angewandte Chemie International Edition, 2020, 59 (51), pp.23213-23219. ⟨10.1002/anie.202009219⟩

Article dans une revue 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 et al.

Protein Science, 2020, 29 (1), pp.237-246. ⟨10.1002/pro.3773⟩

Article dans une revue hal-02370955v1
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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

Article dans une revue hal-02946000v1
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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⟩

Article dans une revue hal-02939019v1
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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⟩

Article dans une revue hal-02345034v1
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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⟩

Article dans une revue hal-02345043v1
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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⟩

Article dans une revue hal-02345040v1
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Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Xavier Martinez , Michael Krone , Naif Alharbi , Alexander Rose , Robert Laramee et al.

Structure, 2019, 27 (11), pp.1617-1623. ⟨10.1016/j.str.2019.09.001⟩

Article dans une revue hal-02370947v1
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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⟩

Article dans une revue 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 et 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
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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 et al.

Scientific Reports, 2019, 9, pp.16450. ⟨10.1038/s41598-019-52760-y⟩

Article dans une revue hal-02370975v1
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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⟩

Article dans une revue hal-02370047v1
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Controlling Redox Enzyme Orientation at Planar Electrodes

Vivek Pratap Hitaishi , Romain Clément , Nicolas Bourassin , Marc Baaden , Anne de Poulpiquet et al.

Catalysts, 2018, 8 (5), pp.192. ⟨10.3390/catal8050192⟩

Article dans une revue hal-01793660v1
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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⟩

Article dans une revue hal-01883877v1
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MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Alexandre Maes , Xavier Martinez , Karen Druart , Benoist Laurent , Sean Guégan et al.

Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180006. ⟨10.1515/jib-2018-0006⟩

Article dans une revue 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 et 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
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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 et al.

Journal of Biological Chemistry, 2018, 293 (18), pp.6637-6646. ⟨10.1074/jbc.M117.809798⟩

Article dans une revue 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⟩

Article dans une revue hal-01935682v1
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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 et 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 Coalson et al.

Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩

Article dans une revue 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⟩

Article dans une revue hal-01935586v1
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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⟩

Article dans une revue hal-01935581v1
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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 et 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 Chen et al.

Faraday Discussions, 2018, 209, pp.83 - 95. ⟨10.1039/C8FD90019A⟩

Article dans une revue hal-01926768v1

Biomimetic water channels: general discussion

Marc Baaden , Mihail Barboiu , Roslyn Bill , Chun-Long Chen , Jeffery Davis et al.

Faraday Discussions, 2018, 209, pp.205 - 229. ⟨10.1039/C8FD90020E⟩

Article dans une revue hal-01926861v1
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Oriented chiral water wires in artificial transmembrane channels

Istvan Kocsis , Mirco Sorci , Heather Vanselous , Samuel Murail , Stephanie Sanders et al.

Science Advances , 2018, 4 (3), pp.eaao5603. ⟨10.1126/sciadv.aao5603⟩

Article dans une revue 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 et al.

Faraday Discussions, 2018, 209, pp.125 - 148. ⟨10.1039/c8fd00046h⟩

Article dans une revue hal-01926847v1
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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 et al.

Scientific Reports, 2017, 7 (1), pp.10217. ⟨10.1038/s41598-017-10687-2⟩

Article dans une revue 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 et 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
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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 et 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
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Visualization of Biomolecular Structures: State of the Art Revisited

B. Kozlíková , M. Krone , M. Falk , N. Lindow , Marc Baaden et al.

Computer Graphics Forum, 2017, 36 (8), pp.178-204. ⟨10.1111/cgf.13072⟩

Article dans une revue hal-01400465v1
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Visual Analysis of Biomolecular Cavities: State of the Art

M. Krone , B. Kozlíková , N. Lindow , Marc Baaden , D. Baum et al.

Computer Graphics Forum, 2016, 35 (3), pp.527 - 551. ⟨10.1111/cgf.12928⟩

Article dans une revue istex hal-01400464v1
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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 et al.

Structure, 2016, 24 (4), pp.595 - 605. ⟨10.1016/j.str.2016.02.014⟩

Article dans une revue hal-01400467v1
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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 et al.

Journal of the American Chemical Society, 2016, 138 (16), pp.5403 - 5409. ⟨10.1021/jacs.6b01811⟩

Article dans une revue hal-01400466v1

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
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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 et 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
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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⟩

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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⟩

Article dans une revue hal-01230766v1
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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 et al.

Structure, 2015, 23 (3), pp.584-97. ⟨10.1016/j.str.2014.12.019⟩

Article dans une revue hal-01230763v1
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Epock : rapid analysis of protein pocket dynamics

Benoist Laurent , Matthieu Chavent , Tristan Cragnolini , Anna Caroline E Dahl , Samuela Pasquali et al.

Bioinformatics, 2015, 31 (9), pp.1478-1480. ⟨10.1093/bioinformatics/btu822⟩

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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⟩

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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 et al.

Faraday Discussions, 2014, 169, pp.45-62. ⟨10.1039/C3FD00134B⟩

Article dans une revue hal-01018071v1
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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 et al.

Faraday Discussions, 2014, Molecular simulations and visualization, 169, pp.119-142. ⟨10.1039/C3FD00142C⟩

Article dans une revue hal-00942627v1

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⟩

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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 et al.

Physical Chemistry Chemical Physics, 2014, 16 (23), pp.11318-11322. ⟨10.1039/C4CP00510D⟩

Article dans une revue hal-01493492v1

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 et al.

Chemical Society Reviews, 2014, 43 (13), pp.4871-4893. ⟨10.1039/c4cs00048j⟩

Article dans une revue hal-04193590v1

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
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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⟩

Article dans une revue hal-01084628v1

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 et al.

Chemical Society Reviews, 2014, pp.4871-93. ⟨10.1039/C4CS00048J⟩

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

Ludovic Sauguet , Frédéric Poitevin , Samuel Murail , Catherine van Renterghem , Gustavo Moraga-Cid et 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

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

Interactive Molecular Dynamics: Scaling up to Large Systems

Matthieu Dreher , Marc Piuzzi , Ahmed Turki , Matthieu Chavent , Marc Baaden et 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

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 et al.

PLoS ONE, 2013, 8 (3), pp.e57990. ⟨10.1371/journal.pone.0057990⟩

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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⟩

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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 Huon et 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-powered tools boost molecular visualization.

Matthieu Chavent , Bruno Lévy , Michael Krone , Katrin Bidmon , Jean-Philippe Nominé et al.

Briefings in Bioinformatics, 2011, 12 (6), pp.689-701. ⟨10.1093/bib/bbq089⟩

Article dans une revue 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⟩

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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 et al.

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

Article dans une revue hal-00645162v1

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⟩

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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 et al.

Nature, 2011, 469 (7330), pp.428-31. ⟨10.1038/nature09647⟩

Article dans une revue hal-00645160v1
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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⟩

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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 et al.

The Journal of Physiology, 2010, 588 (4), pp.565-572. ⟨10.1113/jphysiol.2009.183160⟩

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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 et al.

Journal of Physical Chemistry B, 2010, 114 (43), pp.13839-13846. ⟨10.1021/jp103547s⟩

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General discussion

Marc Baaden

Faraday Discussions, 2010, 144, pp.203-222. ⟨10.1039/B917708F⟩

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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 et al.

Nucleic Acids Research, 2010, 38 (19), pp.6313-23. ⟨10.1093/nar/gkq459⟩

Article dans une revue hal-00533099v1
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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 et 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

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 et al.

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

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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 et al.

ChemBioChem, 2010, 11 (5), pp.653-663. ⟨10.1002/cbic.201000008⟩

Article dans une revue hal-03904748v1

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 Changeux et 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
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Microseconds Dynamics Simulations of the Outer-Membrane Protease T

Marilisa Neri , Marc Baaden , Vincenzo Carnevale , Claudio Anselmi , Amos Maritan et al.

Biophysical Journal, 2008, 94 (1), pp.71-78. ⟨10.1529/biophysj.107.116301⟩

Article dans une revue hal-03904879v1

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

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 Ng et 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 Campbell et 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 Domene et al.

Proteins - Structure, Function and Bioinformatics, 2004, 57 (4), pp.783-791. ⟨10.1002/prot.20257⟩

Article dans une revue istex hal-03907343v1
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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⟩

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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

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

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

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⟩

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

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

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 Tunayar et al.

Inorganic Chemistry, 2000, 39 (10), pp.2033-2041. ⟨10.1021/ic990683n⟩

Article dans une revue istex hal-03920094v1

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
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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 et al.

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

Article dans une revue hal-02956544v1
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Escape from PharmaZ: a Game to Boost Pharmacophore Learning through Immersive Augmented Reality

Iza Marfisi-Schottman , Hubert Santuz , Camille Bisson , Marc Baaden , Nicolas Férey et 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
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UnityMol-Lite: Cross-platform Collaboration and Interactive Methods for Molecular Modeling in XR

Mariano Spivak , Bastien Vincke , Hubert Santuz , Jérôme Hénin , Antoine Taly et 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
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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

Rencontres ThéMoSiA – RCTF2024, Jun 2024, Rouen (FR), France

Communication dans un congrès hal-05368664v1

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 Baaden et al.

3ème réunion pleinière du GDR NADPH Oxydase et Stress oxydant, Nov 2022, Aussois (France), France

Communication dans un congrès 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⟩

Communication dans un congrès 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 et al.

EuroVis 2017 - Short Papers, Jun 2017, Barcelone, Spain. ⟨10.2312/eurovisshort.20171146⟩

Communication dans un congrès 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

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
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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 et 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

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
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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

Communication dans un congrès 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⟩

Communication dans un congrès hal-01498053v1

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
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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

Communication dans un congrès hal-01498083v1
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Interactive Molecular Dynamics: Scaling up to Large Systems

Matthieu Dreher , Marc Piuzzi , Turki Ahmed , Chavent Matthieu , Marc Baaden et al.

International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain

Communication dans un congrès 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

Communication dans un congrès hal-00761683v1
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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

Communication dans un congrès hal-03948334v1
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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
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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

Communication dans un congrès hal-01498124v1

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 et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), 2010, Unknown, France

Communication dans un congrès hal-00953423v1
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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
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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
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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 et al.

Parallel Computing: Architectures, Algorithms and Applications, Sep 2007, Julich, Germany. pp.729-736

Communication dans un congrès 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 et 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

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
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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⟩

Chapitre d'ouvrage hal-04307111v1
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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 et 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
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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⟩

Chapitre d'ouvrage 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 et 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 Freger et 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 Chavent et 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 Baaden et 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
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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

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
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Vitamins : Visual and In Situ Analytics for Molecular Interactive Simulation

Marc Baaden , Matthieu Dreher , Nicolas Ferey , Sébastien Limet , Jessica Prevoteau-Jonquet et al.

2014

Autre publication scientifique hal-01313096v1
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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
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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
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Molecular Modeling with the ChemOffice Ultra 4.5 Program Suite

Marc Baaden

2000

Autre publication scientifique hal-03921142v1