164 citations · 439 across the 5 of their papers we have counts for
5 papers
Automatic learning of hydrogen-bond fixes in an AMBER RNA force field
Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček +5
The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enfor…
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…