665 citations
- Palacký University OlomoucCZ38 papers
- Czech Academy of SciencesCZ19 papers
- FZU ‒ Institute of Physics of the Academy of Sciences of the Czech RepublicCZ16 papers
- Charles UniversityCZ9 papers
- Friedrich-Alexander-Universität Erlangen-NürnbergDE6 papers
- Czech Academy of Sciences, Institute of BiophysicsCZ5 papers
- Scuola Internazionale Superiore di Studi AvanzatiIT5 papers
- University of WarsawPL5 papers
- Czech Academy of Sciences, Institute of Organic Chemistry and BiochemistryCZ4 papers
- King Abdulaziz UniversitySA4 papers
- VSB - Technical University of OstravaCZ4 papers
- Centre National de la Recherche ScientifiqueFR3 papers
4 papers · 1 filter
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…