| Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome J Šponer, P Banáš, P Jurecka, M Zgarbová, P Kührová, M Havrila, ... The journal of physical chemistry letters 5 (10), 1771-1782, 2014 | 180 | 2014 |
| Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact P Florová, P Sklenovsky, P Banas, M Otyepka Journal of chemical theory and computation 6 (11), 3569-3579, 2010 | 149 | 2010 |
| Computer folding of RNA tetraloops: identification of key force field deficiencies P Kuhrova, RB Best, S Bottaro, G Bussi, J Sponer, M Otyepka, P Banas Journal of chemical theory and computation 12 (9), 4534-4548, 2016 | 132 | 2016 |
| Improving the performance of the amber RNA force field by tuning the hydrogen-bonding interactions P Kuhrova, V Mlynsky, M Zgarbová, M Krepl, G Bussi, RB Best, M Otyepka, ... Journal of chemical theory and computation 15 (5), 3288-3305, 2019 | 123 | 2019 |
| Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies J Šponer, G Bussi, P Stadlbauer, P Kührová, P Banáš, B Islam, S Haider, ... Biochimica et Biophysica Acta (BBA)-General Subjects 1861 (5), 1246-1263, 2017 | 108 | 2017 |
| Computer folding of RNA tetraloops? Are we there yet? P Kührová, P Banas, RB Best, J Sponer, M Otyepka Journal of Chemical Theory and Computation 9 (4), 2115-2125, 2013 | 92 | 2013 |
| Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign P Kührová, A De Simone, M Otyepka, RB Best Biophysical journal 102 (8), 1897-1906, 2012 | 76 | 2012 |
| Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration I Beššeová, P Banáš, P Kührová, P Kosinova, M Otyepka, ... The journal of physical chemistry B 116 (33), 9899-9916, 2012 | 73 | 2012 |
| How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes? J Šponer, M Krepl, P Banáš, P Kührová, M Zgarbová, P Jurečka, ... Wiley Interdisciplinary Reviews: RNA 8 (3), e1405, 2017 | 72 | 2017 |
| Insights into stability and folding of GNRA and UNCG tetraloops revealed by microsecond molecular dynamics and well-tempered metadynamics S Haldar, P Kührová, P Banas, V Spiwok, J Sponer, P Hobza, ... Journal of Chemical Theory and Computation 11 (8), 3866-3877, 2015 | 65 | 2015 |
| Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations P Stadlbauer, P Kührová, P Banáš, J Koča, G Bussi, L Trantírek, ... Nucleic acids research 43 (20), 9626-9644, 2015 | 62 | 2015 |
| Understanding RNA flexibility using explicit solvent simulations: the ribosomal and group I intron reverse kink-turn motifs P Sklenovsky, P Florová, P Banas, K Reblova, F Lankas, M Otyepka, ... Journal of Chemical Theory and Computation 7 (9), 2963-2980, 2011 | 59 | 2011 |
| Role of ionizable lipids in SARS-CoV-2 vaccines as revealed by molecular dynamics simulations: from membrane structure to interaction with mRNA fragments M Paloncýová, P Čechová, M Šrejber, P Kührová, M Otyepka The journal of physical chemistry letters 12 (45), 11199-11205, 2021 | 50 | 2021 |
| Are waters around RNA more than just a solvent?–an insight from molecular dynamics simulations P Kührová, M Otyepka, J Šponer, P Banáš Journal of Chemical Theory and Computation 10 (1), 401-411, 2014 | 49 | 2014 |
| Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides V Mlýnský, P Kührová, T Kühr, M Otyepka, G Bussi, P Banás, J Sponer Journal of chemical theory and computation 16 (6), 3936-3946, 2020 | 47 | 2020 |
| Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes P Stadlbauer, P Kührová, L Vicherek, P Banáš, M Otyepka, L Trantírek, ... Nucleic acids research 47 (14), 7276-7293, 2019 | 46 | 2019 |
| Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ Force Field Reparametrizations V Mlýnský, P Kührová, M Zgarbová, P Jurečka, NG Walter, M Otyepka, ... The Journal of Physical Chemistry B 119 (11), 4220-4229, 2015 | 42 | 2015 |
| UUCG RNA tetraloop as a formidable force-field challenge for MD simulations K Mráziková, V Mlýnský, P Kührová, P Pokorná, H Kruse, M Krepl, ... Journal of chemical theory and computation 16 (12), 7601-7617, 2020 | 39 | 2020 |
| Toward convergence in folding simulations of RNA tetraloops: Comparison of enhanced sampling techniques and effects of force field modifications V Mlynsky, M Janeček, P Kuhrova, T Frohlking, M Otyepka, G Bussi, ... Journal of Chemical Theory and Computation 18 (4), 2642-2656, 2022 | 36 | 2022 |
| Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch KC Suddala, IR Price, SS Dandpat, M Janeček, P Kührová, J Šponer, ... Nature Communications 10 (1), 4304, 2019 | 33 | 2019 |
