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Collect. Czech. Chem. Commun. 2011, 76, 457-479
https://doi.org/10.1135/cccc2011035
Published online 2011-04-20 08:33:27

On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

Adam Pecina, Ondřej Přenosil, Jindřich Fanfrlík, Jan Řezáč, Jaroslav Granatier, Pavel Hobza* and Martin Lepšík*

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic

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  • Honda Diego Elias, Martins João Batista Lopes, Ventura Manuel Mateus, Eyrilmez Saltuk Mustafa, Lepšík Martin, Hobza Pavel, Pecina Adam, de Freitas Sonia Maria: Interface Interactions of the Bowman–Birk Inhibitor BTCI in a Ternary Complex with Trypsin and Chymotrypsin Evaluated by Semiempirical Quantum Mechanical Calculations. Eur J Org Chem 2018, 2018, 5203. <https://doi.org/10.1002/ejoc.201800754>
  • Pecina Adam, Meier René, Fanfrlík Jindřich, Lepšík Martin, Řezáč Jan, Hobza Pavel, Baldauf Carsten: The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein–ligand interactions and implicit COSMO solvation. Chem. Commun. 2016, 52, 3312. <https://doi.org/10.1039/C5CC09499B>
  • Vorlová Barbora, Nachtigallová Dana, Jirásková-Vaníčková Jana, Ajani Haresh, Jansa Petr, Řezáč Jan, Fanfrlík Jindřich, Otyepka Michal, Hobza Pavel, Konvalinka Jan, Lepšík Martin: Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study. European Journal of Medicinal Chemistry 2015, 89, 189. <https://doi.org/10.1016/j.ejmech.2014.10.043>
  • Mader Pavel, Pecina Adam, Cígler Petr, Lepšík Martin, Šícha Václav, Hobza Pavel, Grüner Bohumír, Fanfrlík Jindřich, Brynda Jiří, Řezáčová Pavlína: Carborane-Based Carbonic Anhydrase Inhibitors: Insight into CAII/CAIX Specificity from a High-Resolution Crystal Structure, Modeling, and Quantum Chemical Calculations. BioMed Research International 2014, 2014, 1. <https://doi.org/10.1155/2014/389869>
  • Lepšík Martin, Řezáč Jan, Kolář Michal, Pecina Adam, Hobza Pavel, Fanfrlík Jindřich: The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design. ChemPlusChem 2013, 78, 921. <https://doi.org/10.1002/cplu.201300199>
  • Fanfrlík Jindřich, Brahmkshatriya Pathik S, Řezáč Jan, Jílková Adéla, Horn Martin, Mareš Michael, Hobza Pavel, Lepšík Martin: Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors. J. Phys. Chem. B 2013, 117, 14973. <https://doi.org/10.1021/jp409604n>
  • Řezáč Jan, Hobza Pavel: Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J. Chem. Theory Comput. 2012, 8, 141. <https://doi.org/10.1021/ct200751e>