Vojtěch Mlýnský

This paper reparameterizes RNA force fields by replacing hydrogen-bond corrections with Lennard-Jones modifications, improving simulation accuracy without external potentials.

This study evaluates enhanced sampling methods for RNA force field benchmarking using an 8-mer tetraloop, finding T-REMD most robust for accurate folding free energy estimates.

This study compares OPC and TIP4PD water models in simulating structured RNAs, finding they destabilize RNA structures compared to three-point water models.

This paper evaluates RNA force fields by testing their ability to simulate the kink-turn motif, finding that some perform better than others in capturing its structural features.

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.

The paper introduces IDA, a database for storing and integrating MD simulation data, force fields, and experimental measurements to enhance data reuse and FAIR compliance.

This study benchmarks force-field performance for DNA/RNA hybrid duplexes, finding no force field accurately reproduces all structural features and highlighting parameter conflicts.

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.

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 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.

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.