Petr Stadlbauer

This study uses molecular dynamics simulations to investigate whether parallel Holliday junctions exist in solution, finding they are thermodynamically metastable but rarely observed.

This study evaluates RNA force fields using MD simulations of UUCG tetraloops, finding that some recent variants better preserve native structures but still show discrepancies in folding free energy estimates.

This study uses molecular dynamics simulations to explore the folding pathways of an RNA G-quadruplex, revealing multi-pathway mechanisms and highlighting challenges in simulating non-canonical RNA structures.

This study uses pulling simulations to analyze the mechanical stability and unfolding pathways of tetrameric parallel G-quadruplexes, identifying key factors like vertical force components and unfolding transitions.

This study uses molecular dynamics simulations to explore the folding pathways of a parallel G-quadruplex DNA structure, revealing multiple folding paths and limitations of current force fields.

The paper adjusts the AMBER OL3 force field to improve RNA simulations by fixing intra-nucleotide steric clashes in base-phosphate interactions.

This study uses atomistic simulations to observe spontaneous RNA binding to RRM domains of HuR and SRSF1 proteins, revealing dynamic binding pathways and the need for modified force fields.