BibTeX records: Michal Otyepka

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@article{DBLP:journals/jcisd/KuhrovaMOSB23,
  author       = {Petra K{\"{u}}hrov{\'{a}} and
                  Vojtech Ml{\'{y}}nsk{\'{y}} and
                  Michal Otyepka and
                  Jir{\'{\i}} Sponer and
                  Pavel Ban{\'{a}}s},
  title        = {Sensitivity of the {RNA} Structure to Ion Conditions as Probed by
                  Molecular Dynamics Simulations of Common Canonical {RNA} Duplexes},
  journal      = {J. Chem. Inf. Model.},
  volume       = {63},
  number       = {7},
  pages        = {2133--2146},
  year         = {2023},
  url          = {https://doi.org/10.1021/acs.jcim.2c01438},
  doi          = {10.1021/ACS.JCIM.2C01438},
  timestamp    = {Wed, 17 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/KuhrovaMOSB23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/PravdaSVNTBOK18,
  author       = {Luk{\'{a}}s Pravda and
                  David Sehnal and
                  Radka Svobodov{\'{a}} Varekov{\'{a}} and
                  Veronika Navr{\'{a}}tilov{\'{a}} and
                  Dominik Tousek and
                  Karel Berka and
                  Michal Otyepka and
                  Jaroslav Koca},
  title        = {ChannelsDB: database of biomacromolecular tunnels and pores},
  journal      = {Nucleic Acids Res.},
  volume       = {46},
  number       = {Database-Issue},
  pages        = {D399--D405},
  year         = {2018},
  url          = {https://doi.org/10.1093/nar/gkx868},
  doi          = {10.1093/NAR/GKX868},
  timestamp    = {Thu, 23 Sep 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/PravdaSVNTBOK18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/PravdaSTNBBVKO18,
  author       = {Luk{\'{a}}s Pravda and
                  David Sehnal and
                  Dominik Tousek and
                  Veronika Navr{\'{a}}tilov{\'{a}} and
                  V{\'{a}}clav Bazgier and
                  Karel Berka and
                  Radka Svobodov{\'{a}} Varekov{\'{a}} and
                  Jaroslav Koca and
                  Michal Otyepka},
  title        = {MOLEonline: a web-based tool for analyzing channels, tunnels and pores
                  {(2018} update)},
  journal      = {Nucleic Acids Res.},
  volume       = {46},
  number       = {Webserver-Issue},
  pages        = {W368--W373},
  year         = {2018},
  url          = {https://doi.org/10.1093/nar/gky309},
  doi          = {10.1093/NAR/GKY309},
  timestamp    = {Thu, 23 Sep 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/PravdaSTNBBVKO18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/ZgarbovaJLCSO17,
  author       = {Marie Zgarbov{\'{a}} and
                  Petr Jurecka and
                  Filip Lankas and
                  Thomas E. Cheatham III and
                  Jir{\'{\i}} Sponer and
                  Michal Otyepka},
  title        = {Influence of {BII} Backbone Substates on {DNA} Twist: {A} Unified
                  View and Comparison of Simulation and Experiment for All 136 Distinct
                  Tetranucleotide Sequences},
  journal      = {J. Chem. Inf. Model.},
  volume       = {57},
  number       = {2},
  pages        = {275--287},
  year         = {2017},
  url          = {https://doi.org/10.1021/acs.jcim.6b00621},
  doi          = {10.1021/ACS.JCIM.6B00621},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/ZgarbovaJLCSO17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcc/BazgierBOB16,
  author       = {V{\'{a}}clav Bazgier and
                  Karel Berka and
                  Michal Otyepka and
                  Pavel Ban{\'{a}}s},
  title        = {Exponential repulsion improves structural predictability of molecular
                  docking},
  journal      = {J. Comput. Chem.},
  volume       = {37},
  number       = {28},
  pages        = {2485--2494},
  year         = {2016},
  url          = {https://doi.org/10.1002/jcc.24473},
  doi          = {10.1002/JCC.24473},
  timestamp    = {Wed, 01 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcc/BazgierBOB16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/NavratilovaPKBO15,
  author       = {Veronika Navr{\'{a}}tilov{\'{a}} and
                  Mark{\'{e}}ta Palonc{\'{y}}ov{\'{a}} and
                  Michaela Kajsov{\'{a}} and
                  Karel Berka and
                  Michal Otyepka},
  title        = {Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome
                  {P450} 3A4},
  journal      = {J. Chem. Inf. Model.},
  volume       = {55},
  number       = {3},
  pages        = {628--635},
  year         = {2015},
  url          = {https://doi.org/10.1021/ci500645k},
  doi          = {10.1021/CI500645K},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/NavratilovaPKBO15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/PravdaBVSBLKO14,
  author       = {Luk{\'{a}}s Pravda and
                  Karel Berka and
                  Radka Svobodov{\'{a}} Varekov{\'{a}} and
                  David Sehnal and
                  Pavel Ban{\'{a}}s and
                  Roman A. Laskowski and
                  Jaroslav Koca and
                  Michal Otyepka},
  title        = {Anatomy of enzyme channels},
  journal      = {{BMC} Bioinform.},
  volume       = {15},
  pages        = {379},
  year         = {2014},
  url          = {https://doi.org/10.1186/s12859-014-0379-x},
  doi          = {10.1186/S12859-014-0379-X},
  timestamp    = {Thu, 23 Sep 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/PravdaBVSBLKO14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcheminf/SehnalVBPNBIOK13,
  author       = {David Sehnal and
                  Radka Svobodov{\'{a}} Varekov{\'{a}} and
                  Karel Berka and
                  Luk{\'{a}}s Pravda and
                  Veronika Navr{\'{a}}tilov{\'{a}} and
                  Pavel Ban{\'{a}}s and
                  Crina{-}Maria Ionescu and
                  Michal Otyepka and
                  Jaroslav Koca},
  title        = {{MOLE} 2.0: advanced approach for analysis of biomacromolecular channels},
  journal      = {J. Cheminformatics},
  volume       = {5},
  pages        = {39},
  year         = {2013},
  url          = {http://www.jcheminf.com/content/5/1/39},
  timestamp    = {Wed, 13 Aug 2014 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcheminf/SehnalVBPNBIOK13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/BerkaHSBNJIVKO12,
  author       = {Karel Berka and
                  Ondrej Han{\'{a}}k and
                  David Sehnal and
                  Pavel Ban{\'{a}}s and
                  Veronika Navr{\'{a}}tilov{\'{a}} and
                  Deepti Jaiswal Kundu and
                  Crina{-}Maria Ionescu and
                  Radka Svobodov{\'{a}} Varekov{\'{a}} and
                  Jaroslav Koca and
                  Michal Otyepka},
  title        = {MOLE\emph{online} 2.0: interactive web-based analysis of biomacromolecular
                  channels},
  journal      = {Nucleic Acids Res.},
  volume       = {40},
  number       = {Web-Server-Issue},
  pages        = {222--227},
  year         = {2012},
  url          = {https://doi.org/10.1093/nar/gks363},
  doi          = {10.1093/NAR/GKS363},
  timestamp    = {Thu, 23 Sep 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/BerkaHSBNJIVKO12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcamd/DobesFROH11,
  author       = {Petr Dobes and
                  Jindrich Fanfrl{\'{\i}}k and
                  Jan Rez{\'{a}}c and
                  Michal Otyepka and
                  Pavel Hobza},
  title        = {Transferable scoring function based on semiempirical quantum mechanical
                  {PM6-DH2} method: {CDK2} with 15 structurally diverse inhibitors},
  journal      = {J. Comput. Aided Mol. Des.},
  volume       = {25},
  number       = {3},
  pages        = {223--235},
  year         = {2011},
  url          = {https://doi.org/10.1007/s10822-011-9413-5},
  doi          = {10.1007/S10822-011-9413-5},
  timestamp    = {Thu, 16 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcamd/DobesFROH11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/PetrekOBKKD06,
  author       = {Martin Petrek and
                  Michal Otyepka and
                  Pavel Ban{\'{a}}s and
                  Pavl{\'{\i}}na Kosinov{\'{a}} and
                  Jaroslav Koca and
                  Jir{\'{\i}} Damborsk{\'{y}}},
  title        = {{CAVER:} a new tool to explore routes from protein clefts, pockets
                  and cavities},
  journal      = {{BMC} Bioinform.},
  volume       = {7},
  pages        = {316},
  year         = {2006},
  url          = {https://doi.org/10.1186/1471-2105-7-316},
  doi          = {10.1186/1471-2105-7-316},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/PetrekOBKKD06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcamd/BanasOJPD06,
  author       = {Pavel Ban{\'{a}}s and
                  Michal Otyepka and
                  Petr Jer{\'{a}}bek and
                  Martin Petrek and
                  Jir{\'{\i}} Damborsk{\'{y}}},
  title        = {Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant
                  haloalkane dehalogenase revealed by molecular modeling},
  journal      = {J. Comput. Aided Mol. Des.},
  volume       = {20},
  number       = {6},
  pages        = {375--383},
  year         = {2006},
  url          = {https://doi.org/10.1007/s10822-006-9071-1},
  doi          = {10.1007/S10822-006-9071-1},
  timestamp    = {Thu, 16 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcamd/BanasOJPD06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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