Marc Baaden

Deep-learning predictions of biomolecular structures : persistent limitations and new horizons extended by explicit ion addition

This paper evaluates limitations of deep learning in biomolecular structure prediction, highlighting the benefits of explicit ion modeling for improving conformational accuracy.

Full-Length Structural Modeling of Mitofusins with AlphaFold Reveals a Novel Cross-Type Dimerization and Insights into Oligomerization

The paper uses AlphaFold to generate full-length structural models of mitofusins, revealing a novel cross-type dimerization mode and a new hypothetical mechanism of outer mitochondrial membrane fusion.

From foldamers to functional pores: a force field for oligourea-based desalination channels

This paper develops a CHARMM-based force field for oligourea foldamers to simulate their structural integrity and performance in desalination applications.

Statistical Molecular Interaction Fields: A Fast andInformative Tool for Characterizing RNA and ProteinBinding Pockets

This paper introduces Statistical Molecular Interaction Fields (SMIF) to characterize RNA and protein binding pockets, showing they are fast, informative, and compatible with pharmacophoric models.

NOX transmembrane electron transfer is governed by a subtly balanced, self-adjusting charge distribution

This study uses molecular dynamics simulations to analyze how membrane charge density and protein sequence affect electron transfer thermodynamics in NOX5 isoforms.

Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion

The paper identifies Lys716 in yeast mitofusin Fzo1 as a residue modulating dimer stability and fusion through molecular dynamics simulations and experimental validation.

MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations

The paper indexes and analyzes 250,000 molecular dynamics simulation files to create a search engine prototype for MD data.