Marc Baaden

180
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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-05024222 v1
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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-05039981 v1
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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-04794544 v1
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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-05022271 v1
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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-04568346 v1
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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-04299450 v1
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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-04254566 v2
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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-04306427 v1
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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-04257786 v1
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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-03943290 v1
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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, 2023, 64 (1), pp.26-41. ⟨10.1021/acs.jcim.3c01361⟩
Article dans une revue hal-04306436 v1
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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-04257737 v1
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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-04006531 v1
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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-04306431 v1
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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-04257762 v1
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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-03873725 v1
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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-03413156 v1
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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-03826944 v1
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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-03873706 v1
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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-03294641 v1
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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-03873715 v1
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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-03793308 v1
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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-03873710 v1
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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-02944943 v2
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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-03438495 v1
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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-03382660 v1
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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-03438490 v1
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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-03447181 v1
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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-03410227 v1
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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-03364954 v2
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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-02939019 v1
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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-02397135 v1
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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-03028876 v1
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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-02946006 v1
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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-02370955 v1
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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-02946000 v1
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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-02370717 v1
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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-02345057 v1
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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-02370975 v1
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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-02345043 v1
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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-02345034 v1
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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-02345040 v1
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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-02370947 v1
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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-02370047 v1
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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-01926847 v1

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-01926861 v1
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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-01797309 v1

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-01926896 v1
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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-01935586 v1
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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-01744190 v1
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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-01935581 v1
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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-01793660 v1
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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-01935585 v1
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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-01883877 v1
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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-01644564 v1
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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-01795395 v2
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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-01935682 v1
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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.
Article dans une revue hal-01935588 v1

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-01926768 v1
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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-01581980 v1
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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-01644519 v1

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-01587914 v1
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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-01644525 v1
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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-01400465 v1
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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-01400467 v1
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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-01400464 v1
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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-01400466 v1
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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⟩
Article dans une revue hal-01230764 v1
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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-01230763 v1

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-01498028 v1
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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-01230762 v1
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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⟩
Article dans une revue hal-01230761 v1
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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-01230766 v1
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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-01084628 v1

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⟩
Article dans une revue hal-01084631 v1

Multiscale Simulations Give Insight into the Hydrogen in- and out-Pathways of [NiFe]-Hydrogenases from Aquifex Aeolicus and Desulfovibrio Fructosovorans.

Francesco Oteri , Marc Baaden , Elisabeth Lojou , Sophie Sacquin-Mora
Journal of Physical Chemistry B, 2014, 118 (48), pp.13800-13811. ⟨10.1021/jp5089965⟩
Article dans une revue hal-01084622 v1
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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-01018071 v1
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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-00942627 v1

A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450.

Mian Wang , Marc Baaden , Jianyi Wang , Zhiqun Liang
Journal of Chemical Information and Modeling, 2014, pp.1218-25. ⟨10.1021/ci400660e⟩
Article dans une revue hal-01084632 v1

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-01493492 v1

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-01498081 v1

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-04193590 v1

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-00760127 v1

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-01084646 v1

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-01498088 v1

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-01084652 v1

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-01084643 v1

Coarse-grain modelling of protein-protein interactions.

Marc Baaden , Siewert J Marrink
Current Opinion in Structural Biology, 2013, 23 (6), pp.878-86. ⟨10.1016/j.sbi.2013.09.004⟩
Article dans une revue hal-01084639 v1

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⟩
Article dans une revue hal-01084644 v1

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-00760125 v1

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-00760151 v1

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-00760143 v1

Enzyme closure and nucleotide binding structurally lock guanylate kinase.

Olivier Delalande , Sophie Sacquin-Mora , Marc Baaden
Biophysical Journal, 2011, 101 (6), pp.1440-9. ⟨10.1016/j.bpj.2011.07.048⟩
Article dans une revue hal-00645163 v1

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-00645162 v1

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-00645161 v1

Electrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range.

Laurent J Catoire , Marjorie Damian , Marc Baaden , Eric Guittet , Jean-Louis Banères
Journal of Biomolecular NMR, 2011, 50 (3), pp.191-195. ⟨10.1007/s10858-011-9523-3⟩
Article dans une revue istex hal-03011659 v1

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 istex hal-00645160 v1
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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-03904748 v1

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⟩
Article dans une revue pasteur-02174737 v1
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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-00533099 v1

General discussion

Marc Baaden
Faraday Discussions, 2010, 144, pp.203-222. ⟨10.1039/B917708F⟩
Article dans une revue istex hal-03904767 v1
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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⟩
Article dans une revue hal-00645165 v1
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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⟩
Article dans une revue pasteur-02174745 v1

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⟩
Article dans une revue hal-03904752 v1
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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-00661430 v1

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-00602505 v1

General discussion

Marc Baaden
Faraday Discussions, 2010, 144, pp.445-466. ⟨10.1039/B917710H⟩
Article dans une revue istex hal-03904769 v1

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-00713313 v1

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-02175132 v1

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-03904871 v1

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-03904877 v1
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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-03904879 v1

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-00315180 v1

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-03905209 v1

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-03907341 v1

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-03907343 v1
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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⟩
Article dans une revue hal-03907344 v1

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-02951773 v1

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-03911326 v1

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-03911449 v1

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-03165795 v1

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-03911461 v1

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-03911468 v1

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-03911463 v1

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-03920024 v1

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-03920094 v1

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-03920108 v1

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-03920006 v1

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-03919995 v1
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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-02956544 v1
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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-04794554 v1
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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-04794567 v1

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-04426169 v1
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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-02370900 v1
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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-01644549 v1
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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⟩
Communication dans un congrès hal-01497990 v1

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-01498020 v1
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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-01498023 v1
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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-01498055 v1
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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-01498053 v1
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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-01498083 v1

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-03079239 v1
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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-00809024 v1
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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-00761683 v1
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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-01498124 v1
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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-03948334 v1
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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-03948350 v1

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-00953423 v1
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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-03904907 v1
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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-03904892 v1
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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-03907311 v1
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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-03920295 v1
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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-04307111 v1

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-04799896 v1
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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-02944940 v1

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-03211883 v1
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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-02370021 v1
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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-02944941 v1

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-02370038 v1

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-01498051 v1

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-00760181 v1

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-03977638 v1

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-03904759 v1
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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-03907310 v1

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-03920161 v1
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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-01313096 v1
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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-03948139 v2
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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-03977530 v1
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Molecular Modeling with the ChemOffice Ultra 4.5 Program Suite

Marc Baaden
2000
Autre publication scientifique hal-03921142 v1