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===Research work employing PMFLib===
===Research employing PMFLib===
# Tomecek, J.; Cablova, A.; Hromadkova, A.; Novotny, J.; Marek, R.; Durnik, I.; Kulhanek, P.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Vicha, R. Modes of Micromolar Host-Guest Binding of Beta-Cyclodextrin Complexes Revealed by NMR Spectroscopy in Salt Water. ''J. Org. Chem.'' '''2021''', ''86 (6)'', 4483–4496. [https://doi.org/10.1021/acs.joc.0c02917 doi:10.1021/acs.joc.0c02917].
# Kulkarni, S. G.; Jelinkova, K.; Necas, M.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Kulhanek, P.; Vicha, R. A Photochemical/Thermal Switch Based on 4,4 ’-Bis(Benzimidazolio)Stilbene: Synthesis and Supramolecular Properties. ''ChemPhysChem'' '''2020''', ''21 (18)'', 2084–2095. [https://doi.org/10.1002/cphc.202000472 doi:10.1002/cphc.202000472].
# Bouchal, T.; Durník, I.; Illík, V.; Réblová, K.; Kulhánek, P. Importance of Base-Pair Opening for Mismatch Recognition. ''Nucleic Acids Res.'' '''2020''', ''48 (20)'', 11322–11334. [https://doi.org/10.1093/nar/gkaa896 doi:10.1093/nar/gkaa896].
# Ruzicka, M.; Soucek, R.; Kulhanek, P.; Radova, L.; Fajkusova, L.; Reblova, K. Bending of DNA Duplexes with Mutation Motifs. ''DNA Res.'' '''2019''', ''26 (4)'', 341–352. [https://doi.org/10.1093/dnares/dsz013 doi:10.1093/dnares/dsz013].
# Stepan, J.; Kabelka, I.; Koca, J.; Kulhanek, P. Behavior of BsoBI Endonuclease in the Presence and Absence of DNA. ''J. Mol. Model.'' '''2018''', ''24'' (1), 22. [https://doi.org/10.1007/s00894-017-3557-8 doi:10.1007/s00894-017-3557-8].
# Stepan, J.; Kabelka, I.; Koca, J.; Kulhanek, P. Behavior of BsoBI Endonuclease in the Presence and Absence of DNA. ''J. Mol. Model.'' '''2018''', ''24'' (1), 22. [https://doi.org/10.1007/s00894-017-3557-8 doi:10.1007/s00894-017-3557-8].
# Spackova, N.; Reblova, K. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. ''Genes'' '''2018''', ''9 (7)'', 324. [https://doi.org/10.3390/genes9070324 doi:10.3390/genes9070324].
# Ruzicka, M.; Kulhanek, P.; Radova, L.; Cechova, A.; Spackova, N.; Fajkusova, L.; Reblova, K. DNA Mutation Motifs in the Genes Associated with Inherited Diseases. ''PLoS One'' '''2017''', ''12'' (8), e0182377. [https://doi.org/10.1371/journal.pone.0182377 doi:10.1371/journal.pone.0182377].
# Ruzicka, M.; Kulhanek, P.; Radova, L.; Cechova, A.; Spackova, N.; Fajkusova, L.; Reblova, K. DNA Mutation Motifs in the Genes Associated with Inherited Diseases. ''PLoS One'' '''2017''', ''12'' (8), e0182377. [https://doi.org/10.1371/journal.pone.0182377 doi:10.1371/journal.pone.0182377].
# Janoš, P.; Trnka, T.; Kozmon, S.; Tvaroška, I.; Koča, J. Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on PpGalNAcT2. ''J. Chem. Theory Comput.'' '''2016''', ''12 (12)'', 6062–6076. [https://doi.org/10.1021/acs.jctc.6b00531 doi:10.1021/acs.jctc.6b00531].
# Kumari, M.; Kozmon, S.; Kulhanek, P.; Stepan, J.; Tvarozka, I.; Koca, J. Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. ''J. Phys. Chem. B'' '''2015''', ''119'' (12), 4371-4381. [https://doi.org/10.1021/jp511235f doi:10.1021/jp511235f].
# Kumari, M.; Kozmon, S.; Kulhanek, P.; Stepan, J.; Tvarozka, I.; Koca, J. Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. ''J. Phys. Chem. B'' '''2015''', ''119'' (12), 4371-4381. [https://doi.org/10.1021/jp511235f doi:10.1021/jp511235f].
# Novotny, J.; Kulhanek, P.; Marek, R. Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. ''J. Phys. Chem. Lett.'' '''2012''', ''3'' (13), 1788?1792. [https://doi.org/10.1021/jz300559w doi:10.1021/jz300559w].
# Novotny, J.; Kulhanek, P.; Marek, R. Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. ''J. Phys. Chem. Lett.'' '''2012''', ''3'' (13), 1788?1792. [https://doi.org/10.1021/jz300559w doi:10.1021/jz300559w].
# Mones, L.; Kulhanek, P.; Simon, I.; Laio, A.; Fuxreiter, M. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. ''J. Phys. Chem. B'' '''2009''', ''113'' (22), 7867-7873. [https://doi.org/10.1021/jp9000576 doi:10.1021/jp9000576].
# Mones, L.; Kulhanek, P.; Simon, I.; Laio, A.; Fuxreiter, M. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. ''J. Phys. Chem. B'' '''2009''', ''113'' (22), 7867-7873. [https://doi.org/10.1021/jp9000576 doi:10.1021/jp9000576].
===Adaptive Biasing Method===
===Constrained Dynamics===
===String Method===

Latest revision as of 13:35, 21 July 2021

Navigation: Documentation / References

Research employing PMFLib

  1. Tomecek, J.; Cablova, A.; Hromadkova, A.; Novotny, J.; Marek, R.; Durnik, I.; Kulhanek, P.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Vicha, R. Modes of Micromolar Host-Guest Binding of Beta-Cyclodextrin Complexes Revealed by NMR Spectroscopy in Salt Water. J. Org. Chem. 2021, 86 (6), 4483–4496. doi:10.1021/acs.joc.0c02917.
  2. Kulkarni, S. G.; Jelinkova, K.; Necas, M.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Kulhanek, P.; Vicha, R. A Photochemical/Thermal Switch Based on 4,4 ’-Bis(Benzimidazolio)Stilbene: Synthesis and Supramolecular Properties. ChemPhysChem 2020, 21 (18), 2084–2095. doi:10.1002/cphc.202000472.
  3. Bouchal, T.; Durník, I.; Illík, V.; Réblová, K.; Kulhánek, P. Importance of Base-Pair Opening for Mismatch Recognition. Nucleic Acids Res. 2020, 48 (20), 11322–11334. doi:10.1093/nar/gkaa896.
  4. Ruzicka, M.; Soucek, R.; Kulhanek, P.; Radova, L.; Fajkusova, L.; Reblova, K. Bending of DNA Duplexes with Mutation Motifs. DNA Res. 2019, 26 (4), 341–352. doi:10.1093/dnares/dsz013.
  5. Stepan, J.; Kabelka, I.; Koca, J.; Kulhanek, P. Behavior of BsoBI Endonuclease in the Presence and Absence of DNA. J. Mol. Model. 2018, 24 (1), 22. doi:10.1007/s00894-017-3557-8.
  6. Spackova, N.; Reblova, K. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. Genes 2018, 9 (7), 324. doi:10.3390/genes9070324.
  7. Ruzicka, M.; Kulhanek, P.; Radova, L.; Cechova, A.; Spackova, N.; Fajkusova, L.; Reblova, K. DNA Mutation Motifs in the Genes Associated with Inherited Diseases. PLoS One 2017, 12 (8), e0182377. doi:10.1371/journal.pone.0182377.
  8. Janoš, P.; Trnka, T.; Kozmon, S.; Tvaroška, I.; Koča, J. Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on PpGalNAcT2. J. Chem. Theory Comput. 2016, 12 (12), 6062–6076. doi:10.1021/acs.jctc.6b00531.
  9. Kumari, M.; Kozmon, S.; Kulhanek, P.; Stepan, J.; Tvarozka, I.; Koca, J. Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. J. Phys. Chem. B 2015, 119 (12), 4371-4381. doi:10.1021/jp511235f.
  10. Novotny, J.; Kulhanek, P.; Marek, R. Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. J. Phys. Chem. Lett. 2012, 3 (13), 1788?1792. doi:10.1021/jz300559w.
  11. Mones, L.; Kulhanek, P.; Simon, I.; Laio, A.; Fuxreiter, M. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. J. Phys. Chem. B 2009, 113 (22), 7867-7873. doi:10.1021/jp9000576.
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