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1. Full Text Visualizing Biological Membrane Organization and Dynamics
by Baaden, Marc
Journal of Molecular Biology, ISSN 0022-2836, 05/2019, Volume 431, Issue 10, pp. 1889 - 1919
Biological membranes are fascinating. Santiago Ramón y Cajal, who received the Nobel prize in 1906 together with Camillo Golgi for their work on the nervous... 
lipid bilayer | molecular visualization | Molecular dynamics | Atomic force microscopy | Membrane lipids | Evolution | Life Sciences | Biochemistry, Molecular Biology | Biophysics
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2. Full Text Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges
by Lv, Zhihan and Tek, Alex and Da Silva, Franck and Empereur-mot, Charly and Chavent, Matthieu and Baaden, Marc
PLoS ONE, ISSN 1932-6203, 03/2013, Volume 8, Issue 3, pp. e57990 - 13
The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations... 
MOLECULAR-DYNAMICS | PLAYERS | INTEGRATION | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | SIMULATIONS | BINDING | SCIENTIFIC-RESEARCH | GALACTOSIDASE | REVEALS | Computer Graphics | Research Personnel | Signal Transduction | Video Games | Science | Biology | Static Electricity | Video games | Technology application | International economic relations | Electric fields | Visualization (Computers) | Video game industry | Routines | Visualization | 3-D graphics | Extensibility | RNA polymerase | Source code | Electrostatic properties | Computer & video games | Engines | Computer programs | Personal computers | Proteins | Image quality | Industrial development | E coli | Ergonomics | Rendering | Network topologies | Efficiency | Technology | Applications programs | User interfaces | Motion pictures | Electronic & video games | Life Sciences | Quantitative Methods
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3. Full Text X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation
by Bocquet, Nicolas and Nury, Hugues and Baaden, Marc and Le Poupon, Chantal and Changeux, Jean-Pierre and Delarue, Marc and Corringer, Pierre-Jean
Nature, ISSN 0028-0836, 01/2009, Volume 457, Issue 7225, pp. 111 - 114
Pentameric ligand-gated ion channels from the Cys- loop family mediate fast chemo-electrical transduction(1-3), but the mechanisms of ion permeation and gating... 
DOMAIN | CRYSTAL-STRUCTURE | GATING MECHANISM | AMINO-ACIDS | MULTIDISCIPLINARY SCIENCES | NICOTINIC ACETYLCHOLINE-RECEPTOR | BINDING-SITE | IDENTIFICATION | CYS-LOOP | SELECTIVITY | PERMEATION | Ion Channels - metabolism | Cyanobacteria - chemistry | Protein Structure, Quaternary | Hydrophobic and Hydrophilic Interactions | Models, Molecular | Crystallography, X-Ray | Ligands | Protein Subunits - chemistry | Pectobacterium chrysanthemi - chemistry | Ion Channel Gating | Ion Channels - chemistry | Protein Subunits - metabolism | Physiological aspects | Ion channels | Research | Structure | Cyanobacteria | Membrane proteins | Proteins | Signal transduction | Molecules | Ions | Detergents | Binding sites | Cristallography | Chemical Sciences
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4. Full Text X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
by Nury, Hugues and Van Renterghem, Catherine and Weng, Yun and Tran, Alphonso and Baaden, Marc and Dufresne, Virginie and Changeux, Jean-Pierre and Sonner, James M and Delarue, Marc and Corringer, Pierre-Jean
Nature, ISSN 0028-0836, 01/2011, Volume 469, Issue 7330, pp. 428 - 431
General anaesthetics have enjoyed long and widespread use but their molecular mechanism of action remains poorly understood. There is good evidence that their... 
GLYCINE RECEPTORS | MOLECULAR-DYNAMICS | ALLOSTERIC TRANSITIONS | MULTIDISCIPLINARY SCIENCES | HIGH-RESOLUTION | NICOTINIC ACETYLCHOLINE-RECEPTOR | BINDING-SITE | CRYSTAL-STRUCTURES | GABA(A) RECEPTORS | IDENTIFICATION | MODULATION | Protein Structure, Tertiary | Protons | Anesthetics, General - metabolism | Isoflurane - metabolism | Ligand-Gated Ion Channels - chemistry | Cyanobacteria - chemistry | Isoflurane - chemistry | Mutant Proteins - genetics | Models, Molecular | Crystallography, X-Ray | Mutant Proteins - metabolism | Binding Sites - genetics | Isoflurane - analogs & derivatives | Molecular Dynamics Simulation | Propofol - chemistry | Propofol - metabolism | Ligand-Gated Ion Channels - genetics | Mutant Proteins - chemistry | Protein Binding | Anesthetics, General - chemistry | Ligands | Electrophysiological Phenomena | Ligand-Gated Ion Channels - metabolism | Proteins | Chemical properties | Anesthetics | Structure | Lipids | Binding sites | Ligand-Gated Ion Channels | Neurons and Cognition | Biochemistry, Molecular Biology | Neurobiology | Biophysics | Isoflurane | Mutant Proteins | Life Sciences | Anesthetics, General | Cyanobacteria | Biomolecules | Propofol | Binding Sites
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5. Full Text Coarse-grain modelling of protein–protein interactions
by Baaden, Marc and Marrink, Siewert J
Current Opinion in Structural Biology, ISSN 0959-440X, 12/2013, Volume 23, Issue 6, pp. 878 - 886
Here, we review recent advances towards the modelling of protein–protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely... 
SELF-ASSOCIATION | DOCKING | COMPLEXES | COMPUTER-SIMULATION | FORCE-FIELD | MOLECULAR-DYNAMICS SIMULATIONS | MEMBRANE-PROTEINS | HYDRODYNAMIC INTERACTIONS | LIPID INTERACTIONS | TRANSMEMBRANE HELIX | BIOCHEMISTRY & MOLECULAR BIOLOGY | CELL BIOLOGY | Models, Molecular | Protein Interaction Mapping - methods | Membrane Proteins - metabolism | Membrane Proteins - chemistry | Solubility | Analysis | Models | Protein-protein interactions | Life Sciences | Quantitative Methods
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6. Full Text A locally closed conformation of a bacterial pentameric proton-gated ion channel
by Prevost, Marie S and Sauguet, Ludovic and Nury, Hugues and Van Renterghem, Catherine and Huon, Christèle and Poitevin, Frederic and Baaden, Marc and Delarue, Marc and Corringer, Pierre-Jean
Nature Structural and Molecular Biology, ISSN 1545-9993, 06/2012, Volume 19, Issue 6, pp. 642 - 649
Pentameric ligand-gated ion channels mediate signal transduction through conformational transitions between closed-pore and open-pore states. To stabilize a... 
MOLECULAR-DYNAMICS | MAXIMUM-LIKELIHOOD | DOMAIN | LIGAND-BINDING | BIOCHEMISTRY & MOLECULAR BIOLOGY | X-RAY-STRUCTURE | CELL BIOLOGY | GLYCINE RECEPTORS | REFINEMENT | BIOPHYSICS | NICOTINIC ACETYLCHOLINE-RECEPTOR | BINDING-SITE | TRANSITIONS | Cyanobacteria - genetics | Protons | Amino Acid Sequence | Allosteric Regulation | Cyanobacteria - chemistry | Bacterial Proteins - chemistry | Bacterial Proteins - genetics | Cyanobacteria - metabolism | Ion Channels - genetics | Crystallography, X-Ray | Cysteine - chemistry | Molecular Dynamics Simulation | Cysteine - genetics | Ion Channels - metabolism | Bacterial Proteins - metabolism | Protein Conformation | Cysteine - metabolism | Mutation | Ion Channel Gating | Ion Channels - chemistry | Physiological aspects | Bacteria | Cellular signal transduction | Ion channels | Research | Molecular biology | Crystal structure | Cysteine | Ion Channels | Biochemistry, Molecular Biology | Biophysics | Bacterial Proteins | Life Sciences | Cyanobacteria
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7. Full Text Structural basis for ion permeation mechanism in pentameric ligand‐gated ion channels
by Sauguet, Ludovic and Poitevin, Frédéric and Murail, Samuel and Van Renterghem, Catherine and Moraga‐Cid, Gustavo and Malherbe, Laurie and Thompson, Andrew W and Koehl, Patrice and Corringer, Pierre‐Jean and Baaden, Marc and Delarue, Marc
The EMBO Journal, ISSN 0261-4189, 03/2013, Volume 32, Issue 5, pp. 728 - 741
To understand the molecular mechanism of ion permeation in pentameric ligand‐gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a... 
crystallography | electrophysiology | molecular dynamics | permeation | ion channels | MOLECULAR-DYNAMICS | PROTEIN | POTASSIUM CHANNELS | BIOCHEMISTRY & MOLECULAR BIOLOGY | X-RAY-STRUCTURE | RESOLUTION | CRYSTAL-STRUCTURES | STATE | BROWNIAN DYNAMICS | SELECTIVITY-FILTER | CELL BIOLOGY | NICOTINIC ACETYLCHOLINE-RECEPTOR | Threonine - chemistry | Models, Chemical | Sodium - chemistry | Electrophysiology | Crystallography, X-Ray | Sodium - metabolism | Threonine - metabolism | Threonine - genetics | Protein Structure, Quaternary | Water - chemistry | Female | Xenopus laevis - growth & development | Ligand-Gated Ion Channels - metabolism | Ligand-Gated Ion Channels - chemistry | Oocytes - metabolism | Models, Molecular | Serine - genetics | Mutation - genetics | Serine - chemistry | Serine - metabolism | Molecular Dynamics Simulation | Animals | Xenopus laevis - metabolism | Ligand-Gated Ion Channels - genetics | Hydrophobic and Hydrophilic Interactions | Ligands | Ion Channel Gating | Ions | Molecular biology | Crystals | Life Sciences | Neurons and Cognition
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8. Full Text Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans
by Oteri, Francesco and Baaden, Marc and Lojou, Elisabeth and Sacquin-Mora, Sophie
The Journal of Physical Chemistry B, ISSN 1520-6106, 12/2014, Volume 118, Issue 48, pp. 13800 - 13811
[NiFe]-hydrogenases catalyze the cleavage of molecular hydrogen into protons and electrons and represent promising tools for H2-based technologies such as... 
MOLECULAR-DYNAMICS | ACTIVE-SITE | NICKEL-IRON HYDROGENASE | NIFE HYDROGENASE | CRYSTAL-STRUCTURE | 4FE-3S CLUSTER | CHEMISTRY, PHYSICAL | PROTON TRANSPORT | MEMBRANE-BOUND HYDROGENASE | BROWNIAN DYNAMICS | PROTEIN MECHANICS | Catalytic Domain | Desulfovibrio - enzymology | Hydrogenase - metabolism | Biocatalysis | Oxidation-Reduction | Aquifoliaceae - enzymology | Hydrogenase - chemistry | Static Electricity | Hydrogen - chemistry | Hydrogen - metabolism | Molecular Dynamics Simulation | Nickel compounds | Iron compounds | Chemical properties | Hydrogenation | Analysis | Residues | Enzymes | Dynamic tests | Pathways | Dynamic mechanical properties | Dynamics | Desulfovibrio | Oxidation | or physical chemistry | Chemical Sciences | Theoretical and
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9. Full Text Ten simple rules to create a serious game, illustrated with examples from structural biology
by Baaden, Marc and Delalande, Olivier and Ferey, Nicolas and Pasquali, Samuela and Waldispühl, Jérôme and Taly, Antoine
PLoS Computational Biology, ISSN 1553-734X, 03/2018, Volume 14, Issue 3, p. e1005955
The Foldit project is an online 3D jigsaw puzzle in which players are invited to shake and wiggle the 3D structure of proteins to find their most stable... 
ROSETTA | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Educational games | Methods | Crowdsourcing | Studies | Researchers | Designers | Funding | Instructional design | Genomics | Science | Software | Biology | Computer & video games | Life Sciences | Genetics
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10. Full Text One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue
by Hugues Nury and Frédéric Poitevin and Catherine Van Renterghem and Jean-Pierre Changeux and Pierre-Jean Corringer and Marc Delarue and Marc Baaden
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 4/2010, Volume 107, Issue 14, pp. 6275 - 6280
Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the Gloeobacter violaceus receptor (GLIC), are... 
Receptors | Crystals | Molecular dynamics | Ions | Ligand gated ion channels | Agonists | Ion channels | Nicotinic receptors | Crystal structure | Hydrophobic gate | Allosteric transition | Cys-loop receptor family | GATED ION-CHANNEL | DOMAIN | allosteric transition | CYS-LOOP RECEPTOR | MECHANISM | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | X-RAY-STRUCTURE | cys-loop receptor family | STATE | ACETYLCHOLINE-RECEPTOR | PORE | hydrophobic gate | BINDING | Protein Structure, Tertiary | Receptors, Nicotinic - metabolism | Protein Structure, Secondary | Cyanobacteria - chemistry | Bacterial Proteins - chemistry | Cyanobacteria - metabolism | Models, Molecular | Crystallography, X-Ray | Molecular Dynamics Simulation | Receptors, Nicotinic - chemistry | Time Factors | Bacterial Proteins - metabolism | Ion Channel Gating | Hydrogen-Ion Concentration | Physiological aspects | Research | Receptors, Nicotinic | Biochemistry, Molecular Biology | Bacterial Proteins | Life Sciences | Cyanobacteria | Biological Sciences
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11. Full Text Visualization of Biomolecular Structures: State of the Art Revisited
by Kozlíková, B and Krone, M and Falk, M and Lindow, N and Baaden, M and Baum, D and Viola, I and Parulek, J and Hege, H.‐C and Institutionen för teknik och naturvetenskap and Medie- och Informationsteknik and Linköpings universitet and Tekniska fakulteten
Computer Graphics Forum, ISSN 0167-7055, 12/2017, Volume 36, Issue 8, pp. 178 - 204
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed... 
solid | surface | bioinformatics visualization | and object representations | Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modelling—Curve | molecular visualization | taxonomy | MOLECULAR-DYNAMICS | ENVIRONMENT |