List of works - Marc Baaden

A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin

scientific article published on 04 September 2019

A VR framework for interacting with molecular simulations

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

scientific article

A locally closed conformation of a bacterial pentameric proton-gated ion channel

scientific article

A membrane-inserted structural model of the yeast mitofusin Fzo1. ⬇️

scientific article published on 31 August 2017

A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.

scientific article published in August 2003

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure

scientific article

Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network

scientific article published in Scientific Reports

Applications to water transport systems: general discussion

scientific article published on 01 September 2018

Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues.

scientific article published on 07 December 2009

Biomimetic approach for highly selective artificial water channels based on tubular Pillar[5]Arene dimers

scientific article published on 09 September 2020

Biomimetic water channels: general discussion

scientific article published on 01 September 2018

Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes.

scientific article

Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study

scientific article published on 02 January 2020

Coarse-grain modelling of protein-protein interactions

scientific article

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

scientific article published in July 2009

Complex molecular assemblies at hand via interactive simulations

scientific article

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

scientific article

Controlling Redox Enzyme Orientation at Planar Electrodes

Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions.

scientific article published on 13 March 2018

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

scientific article published on 19 June 2011

Enzyme closure and nucleotide binding structurally lock guanylate kinase.

scientific article

Epock: rapid analysis of protein pocket dynamics.

scientific article published on 12 December 2014

ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

scientific article

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.

scientific article published in April 2003

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations

scientific article

From Virtual Reality to Immersive Analytics in Bioinformatics

scientific article published on 09 July 2018

Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress

scientific article published on November 2010

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

scientific article published on 7 July 2011

GPU-powered tools boost molecular visualization

scientific article published on 09 February 2011

Game on, science - how video game technology may help biologists tackle visualization challenges

scientific article

Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates

scientific article published on 26 November 2019

Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK

scientific article published on 14 March 2019

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution

scientific article published on 20 December 2017

How cations can assist DNase I in DNA binding and hydrolysis

scientific article

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grain Representation

scientific article published on 14 September 2020

Interactions between neuronal fusion proteins explored by molecular dynamics

scientific article published on 22 January 2008

Itinéraires bis ⬇️

book published in 2009

Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations

article

Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic

scientific article published in 2021

Membrane protein structure quality in molecular dynamics simulation.

scientific article

Microseconds dynamics simulations of the outer-membrane protease T

scientific article

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

scientific article published on 21 June 2018

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk

scientific article published on 15 June 2012

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

scientific article

Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

scientific article published on 11 November 2019

Molecular Dynamics Study of the Uranyl Extraction by Tri-n-butylphosphate (TBP): Demixing of Water/“Oil”/TBP Solutions with a Comparison of Supercritical CO2and Chloroform

article

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

scientific article published on 26 September 2019

Molecular Modeling as the Spark for Active Learning Approaches for Interdisciplinary Biology Teaching

Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching

scientific article published on 19 April 2019

Molecular simulations and visualization: introduction and overview

scientific article published on 6 October 2014

Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device

scientific article published on 01 January 2010

Multi-scale simulations of biological systems using the OPEP coarse-grained model.

scientific article published on 13 September 2017

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

scientific article published on 21 November 2014

Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion.

scientific article

OmpT: molecular dynamics simulations of an outer membrane enzyme

scientific article

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

scientific article

Oriented chiral water wires in artificial transmembrane channels.

scientific article published on 23 March 2018

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

scientific article

Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination

scientific article

Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking

scientific article published on 12 July 2019

Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.

scientific article published on 12 May 2017

Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation

scientific article published on 10 April 2016

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

scientific article published on 09 July 2018

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

scientific article

String method solution of the gating pathways for a pentameric ligand-gated ion channel.

scientific article published on 9 May 2017

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

scientific article

Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking

scientific article published on 31 August 2019

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

scientific article published on 01 September 2018

Taming molecular flexibility to tackle rare diseases.

scientific article published on 2 April 2015

Ten simple rules to create a serious game, illustrated with examples from structural biology.

scientific article

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

scientific article published on 23 April 2014

The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation

scientific article published on 19 July 2018

The modelling and enhancement of water hydrodynamics: general discussion

scientific article published on 01 September 2018

The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif

scientific article published on November 2010

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

scientific article published on 01 June 2014

Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database

article

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software

scientific article published on 4 December 2014

Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces

scientific article published on 27 September 2012

UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

scientific article published on 28 May 2021

Visualizing Biological Membrane Organization and Dynamics

scientific article published on 04 March 2019

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

scientific article published on 25 November 2019

Visualizing protein structures - tools and trends

scientific article published on 20 March 2020

Water permeation across artificial I-quartet membrane channels: from structure to disorder

scientific article published on 01 September 2018

What Can Human-Guided Simulations Bring to RNA Folding?

scientific article published on 22 June 2017

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

scientific article

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

scientific article

List of works by Marc Baaden

A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin

A VR framework for interacting with molecular simulations

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

A locally closed conformation of a bacterial pentameric proton-gated ion channel

A membrane-inserted structural model of the yeast mitofusin Fzo1. ⬇️

A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure

Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network

Applications to water transport systems: general discussion

Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues.

Biomimetic approach for highly selective artificial water channels based on tubular Pillar[5]Arene dimers

Biomimetic water channels: general discussion

Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes.

Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study

Coarse-grain modelling of protein-protein interactions

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

Complex molecular assemblies at hand via interactive simulations

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

Controlling Redox Enzyme Orientation at Planar Electrodes

Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions.

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

Enzyme closure and nucleotide binding structurally lock guanylate kinase.

Epock: rapid analysis of protein pocket dynamics.

ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations

From Virtual Reality to Immersive Analytics in Bioinformatics

Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

GPU-powered tools boost molecular visualization

Game on, science - how video game technology may help biologists tackle visualization challenges

Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates

Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution

How cations can assist DNase I in DNA binding and hydrolysis

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grain Representation

Interactions between neuronal fusion proteins explored by molecular dynamics

Itinéraires bis ⬇️

Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations

Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic

Membrane protein structure quality in molecular dynamics simulation.

Microseconds dynamics simulations of the outer-membrane protease T

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

Molecular Dynamics Study of the Uranyl Extraction by Tri-n-butylphosphate (TBP): Demixing of Water/“Oil”/TBP Solutions with a Comparison of Supercritical CO2and Chloroform

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Molecular Modeling as the Spark for Active Learning Approaches for Interdisciplinary Biology Teaching

Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching

Molecular simulations and visualization: introduction and overview

Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device

Multi-scale simulations of biological systems using the OPEP coarse-grained model.

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion.

OmpT: molecular dynamics simulations of an outer membrane enzyme

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

Oriented chiral water wires in artificial transmembrane channels.

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination

Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking

Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.

Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

String method solution of the gating pathways for a pentameric ligand-gated ion channel.

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

Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking

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

Taming molecular flexibility to tackle rare diseases.

Ten simple rules to create a serious game, illustrated with examples from structural biology.

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation

The modelling and enhancement of water hydrodynamics: general discussion

The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software

Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces