164 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Scuola Internazionale Superiore di Studi AvanzatiIT7 papers
- Czech Academy of SciencesCZ6 papers
- Palacký University OlomoucCZ5 papers
- Regional Centre of Advanced Technologies and MaterialsCZ5 papers
- Centre National de la Recherche ScientifiqueFR3 papers
- Central European Institute of Technology – Masaryk UniversityCZ2 papers
- Czech Academy of Sciences, Heyrovsky InstituteCZ2 papers
- Heidelberg UniversityDE2 papers
- InsermFR2 papers
- Lyon 1 UniversitéFR2 papers
- Masaryk UniversityCZ2 papers
- Technical University of MunichDE2 papers
7 papers · 1 filter
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Valerio Piomponi, Miroslav Krepl, Jiri Sponer +1
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT…
RNA Dynamics from Experimental and Computational Approaches
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka +16
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining…
Do conformational changes contribute to the surface plasmon resonance signal?
Daniel Dobrovodský, Carmelo Di Primo
Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for in…
Folding of guanine quadruplex molecules -- funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
Jiří Šponer, Giovanni Bussi, Petr Stadlbauer +6
Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural stud…
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kührová, Robert B. Best, Sandro Bottaro +4
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motif…
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
Sandro Bottaro, Pavel Banáš, Jiri Sponer +1
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the fol…
Hairpins Participating in Folding of Human Telomeric Sequence Quadruplexes Studied by Standard and T-REMD Simulations
Petr Stadlbauer, Petra Kührová, Pavel Banáš +5
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting…