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
Showing 2016Show all
3 papers · 1 filter
q-bio.BM2016★ 125 cited
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…
q-bio.BM2016★ 164 cited
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…
q-bio.BM2016★ 106 cited
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…