| Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles M Zgarbová, M Otyepka, J Šponer, A Mládek, P Banáš, ... Journal of chemical theory and computation, 2011 | 1046 | 2011 |
| Promoting transparency and reproducibility in enhanced molecular simulations Nature methods 16 (8), 670-673, 2019 | 811 | 2019 |
| CAVER: a new tool to explore routes from protein clefts, pockets and cavities M Petřek, M Otyepka, P Banáš, P Košinová, J Koča, J Damborský BMC bioinformatics 7, 1-9, 2006 | 649 | 2006 |
| RNA structural dynamics as captured by molecular simulations: a comprehensive overview J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro, RA Cunha, A Gil-Ley, ... Chemical reviews 118 (8), 4177-4338, 2018 | 506 | 2018 |
| Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins P Banáš, D Hollas, M Zgarbová, P Jurečka, M Orozco, TE Cheatham III, ... Journal of Chemical Theory and Computation, 2010 | 408 | 2010 |
| MOLE 2.0: advanced approach for analysis of biomacromolecular channels D Sehnal, R Svobodová Vařeková, K Berka, L Pravda, V Navrátilová, ... Journal of cheminformatics 5, 1-13, 2013 | 339 | 2013 |
| Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate M Pavlova, M Klvana, Z Prokop, R Chaloupkova, P Banas, M Otyepka, ... Nature chemical biology 5 (10), 727-733, 2009 | 323 | 2009 |
| Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA, and Z-DNA M Krepl, M Zgarbová, P Stadlbauer, M Otyepka, P Banas, J Koca, ... Journal of chemical theory and computation 8 (7), 2506-2520, 2012 | 286 | 2012 |
| 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 | 179 | 2014 |
| MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels K Berka, O Hanák, D Sehnal, P Banáš, V Navratilova, D Jaiswal, ... Nucleic acids research 40 (W1), W222-W227, 2012 | 156 | 2012 |
| 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 |
| Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment J Šponer, JE Šponer, A Mládek, P Jurečka, P Banáš, M Otyepka Biopolymers 99 (12), 978-988, 2013 | 147 | 2013 |
| Anatomy of enzyme channels L Pravda, K Berka, R Svobodová Vařeková, D Sehnal, P Banáš, ... BMC bioinformatics 15, 1-8, 2014 | 141 | 2014 |
| 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 |
| Reactivity of fluorographene: a facile way toward graphene derivatives M Dubecký, E Otyepková, P Lazar, F Karlický, M Petr, K Čépe, ... The journal of physical chemistry letters 6 (8), 1430-1434, 2015 | 117 | 2015 |
| 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 |
| Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM P Banáš, P Jurečka, NG Walter, J Šponer, M Otyepka Methods 49 (2), 202-216, 2009 | 104 | 2009 |
| The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies J Šponer, A Mládek, JE Šponer, D Svozil, M Zgarbová, P Banáš, ... Physical Chemistry Chemical Physics 14 (44), 15257-15277, 2012 | 97 | 2012 |
| Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme V Mlýnský, P Banáš, D Hollas, K Réblová, NG Walter, J Šponer, ... The Journal of Physical Chemistry B 114 (19), 6642-6652, 2010 | 97 | 2010 |
Michal OtyepkaCATRIN, Palacký University; IT4Innovations, VŠB Technical University of OstravaVerified email at upol.cz
