Jiřı́ Šponer

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

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 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 shows that ammonium and alkylammonium counterions enhance RNA polymerization from 2,3-cyclic nucleotides under dry, geologically plausible conditions.

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

This study uses molecular dynamics simulations to show that U:U mismatches in RNA adopt multiple conformations influenced by neighboring base pairs and environmental factors.

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 show how TbRGG2 RRM binds uridine-rich RNAs through dynamic binding modes and auxiliary states, enabling efficient scanning while maintaining selectivity.

The paper identifies two conserved residues in Hfq critical for stabilizing small regulatory RNAs under nitrogen starvation.

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 refines the AMBER DNA force field parameters to better model A-DNA stability and improve protein-DNA complex modeling.

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 paper identifies the RNA binding specificity of Hrp48, showing it binds the msl-2 mRNA 3' UTR independently of Sxl and Unr downstream of their binding sites.

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.

The paper uses molecular dynamics simulations to study RNA-FUS interactions, revealing conformational heterogeneity and dynamic behavior that complement experimental data.

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.