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Michal Otyepka

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Pavlína Podloucká; Karel Berka; Jean-Luc Duroux; Gabin Fabre; Michal Otyepka; Markéta Paloncýová; Patrick Trouillas
Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant.
Arnošt Mládek; Michal Otyepka; Daniel Svozil; Marie Zgarbová; Pavel Banáš; Petr Cech; Petr Jurečka; Miroslav Krepl; Jiří Sponer
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.
Petr Lazar; Petr Jurečka; František Karlický; Mikuláš Kocman; Eva Otyepková; Klára Safářová; Michal Otyepka
Adsorption of small organic molecules on graphene.

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All Publications

2013: Pavlína Podloucká; Karel Berka; Jean-Luc Duroux; Gabin Fabre; Michal Otyepka; Markéta Paloncýová; Patrick Trouillas
Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant.
The journal of physical chemistry. B 2013;117(17):5043-9.
2013: Arnošt Mládek; Michal Otyepka; Daniel Svozil; Marie Zgarbová; Pavel Banáš; Petr Cech; Petr Jurečka; Miroslav Krepl; Jiří Sponer
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.
Physical chemistry chemical physics : PCCP 2013;15(19):7295-310.
2013: Petr Lazar; Petr Jurečka; František Karlický; Mikuláš Kocman; Eva Otyepková; Klára Safářová; Michal Otyepka
Adsorption of small organic molecules on graphene.
Journal of the American Chemical Society 2013;135(16):6372-7.
2013: Markéta Paloncýová; Karel Berka; Michal Otyepka
Molecular insight into affinities of drugs and their metabolites to lipid bilayers.
The journal of physical chemistry. B 2013;117(8):2403-10.
2013: Petr Lazar; Qiang Li; Klára Safářová; Radek Zbořil; Shuai Zhang; Flemming Besenbacher; Mingdong Dong; Jens Peter Froning; Jaroslav Granatier; Pavel Hobza; Michal Otyepka
Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions.
ACS nano 2013;7(2):1646-51.
2013: Miroslav Krepl; Michal Otyepka; Pavel Banáš; Jiří Šponer
Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study.
The journal of physical chemistry. B 2013;117(6):1872-9.
2012: Jiří Šponer; Judit E Šponer; Daniel Svozil; Marie Zgarbová; Pavel Banáš; Petr Jurečka; Arnošt Mládek; Michal Otyepka
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.
Physical chemistry chemical physics : PCCP 2012;14(44):15257-77.
2012: Vasilios Georgakilas; Pavel Hobza; K Christian Kemp; Athanasios B Bourlinos; Vimlesh Chandra; Namdong Kim; Michal Otyepka; Radek Zboril; Kwang S Kim
Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications.
Chemical reviews 2012;112(11):6156-214.
2012: Pavel Banáš; Petr Sklenovský; Joseph E Wedekind; Jirí Sponer; Michal Otyepka
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.
The journal of physical chemistry. B 2012;116(42):12721-34.
2012: Ivana Beššeová; Pavlína Košinová; Petra Kührová; Michal Otyepka; Pavel Banáš; Jiří Šponer
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.
The journal of physical chemistry. B 2012;116(33):9899-916.
2012: František Karlický; Radek Zbořil; Michal Otyepka
Band gaps and structural properties of graphene halides and their derivates: a hybrid functional study with localized orbital basis sets.
The Journal of chemical physics 2012;137(3):034709.
2012: Karel Berka; Ondrej Hanák; Crina-Maria Ionescu; Deepti Jaiswal; Jaroslav Koca; Veronika Navrátilová; David Sehnal; Radka Svobodová Vareková; Pavel Banás; Michal Otyepka
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.
Nucleic acids research 2012;40(Web Server issue):W222-7.
2012: Karel Berka; Tereza Hendrychová; Reinhard Lange; Vlastimil Mašek; Pavel Anzenbacher; Eva Anzenbacherová; Michal Otyepka
Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site.
Journal of inorganic biochemistry 2012;110():46-50.
2012: Petra Kührová; Michal Otyepka; Alfonso De Simone; Robert B Best
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign.
Biophysical journal 2012;102(8):1897-906.
2012: Pavlína Košinová; Michal Otyepka; Karel Berka; Michael Wykes; Patrick Trouillas
Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition.
The journal of physical chemistry. B 2012;116(4):1309-18.
2012: Pavel Anzenbacher; Michal Otyepka
Editorial: cytochromes P450: flexibility and plasticity - properties determining substrate preferences.
Current drug metabolism 2012;13(2):129.
2012: Tereza Hendrychova; Veronika Navratilova; Pavel Anzenbacher; Karel Berka; Michal Otyepka
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations.
Current drug metabolism 2012;13(2):177-89.
2012: Michal Otyepka; Karel Berka; Pavel Anzenbacher
Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?
Current drug metabolism 2012;13(2):130-42.
2011: Vojtěch Mlýnský; Jiří Šponer; Nils G Walter; Pavel Banáš; Michal Otyepka
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.
The journal of physical chemistry. B 2011;115(47):13911-24.
2011: Marie Zgarbová; Craig L Zirbel; Judit E Sponer; Pavel Banáš; Petr Jurečka; Neocles Leontis; Michal Otyepka; Jirí Sponer
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.
The journal of physical chemistry. A 2011;115(41):11277-92.
2011: Karel Berka; Tereza Hendrychová; Pavel Anzenbacher; Michal Otyepka
Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site.
The journal of physical chemistry. A 2011;115(41):11248-55.
2011: Petr Dobes; Jindrich Fanfrlík; Michal Otyepka; Jan Rezác; Pavel Hobza
Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-inhibitor complexes involving halogen bonds well, while the empirical potential fails.
The journal of physical chemistry. B 2011;115(26):8581-9.
2011: Petr Dobeš; Jindřich Fanfrlík; Jan Rezáč; Michal Otyepka; Pavel Hobza
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
Journal of computer-aided molecular design 2011;25(3):223-35.
2011: Karel Berka; Michal Otyepka
Insenstivity to close contacts and inability to predict protein foldability.
Journal of biomolecular structure & dynamics 2011;28(4):633-4; discussion 669-674.
2011: Tereza Hendrychová; Eva Anzenbacherová; Jiří Hudeček; Josef Skopalík; Reinhard Lange; Peter Hildebrandt; Michal Otyepka; Pavel Anzenbacher
Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations.
Biochimica et biophysica acta 2011;1814(1):58-68.
2010: Radek Zbořil; František Karlický; Athanasios B Bourlinos; Theodore A Steriotis; Athanasios K Stubos; Vasilios Georgakilas; Klára Šafářová; Dalibor Jančík; Christos Trapalis; Michal Otyepka
Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene.
Small (Weinheim an der Bergstrasse, Germany) 2010;6(24):2885-91.
2010: Marie Zgarbová; Michal Otyepka; Jirí Sponer; Pavel Hobza; Petr Jurecka
Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.
Physical chemistry chemical physics : PCCP 2010;12(35):10476-93.
2010: Pavel Banás; Nils Walter; Jirí Sponer; Michal Otyepka
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.
The journal of physical chemistry. B 2010;114(26):8701-12.
2010: Emma S Child; Tereza Hendrychová; Karen McCague; Andy Futreal; Michal Otyepka; David J Mann
A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding.
Biochimica et biophysica acta 2010;1803(7):858-64.
2010: Vojtech Mlýnský; Pavel Banás; Daniel Hollas; Kamila Réblová; Nils Walter; Jirí Sponer; Michal Otyepka
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.
The journal of physical chemistry. B 2010;114(19):6642-52.
2010: Klára Dvoráková-Holá; Anna Matusková; Martin Kubala; Michal Otyepka; Tomáš Kučera; Jaroslav Vecer; Petr Herman; Natalya Parkhomenko; Eva Kutejova; Jiri Janata
Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20.
Journal of molecular biology 2010;396(5):1197-210.
2010: Judit E Sponer; Alvaro Vázquez-Mayagoitia; Bobby G Sumpter; Jerzy Leszczynski; Jirí Sponer; Michal Otyepka; Pavel Banás; Miguel Fuentes-Cabrera
Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues.
Chemistry (Weinheim an der Bergstrasse, Germany) 2010;16(10):3057-65.
2010: P Sklenovsý; Michal Otyepka
In silico structural and functional analysis of fragments of the ankyrin repeat protein p18(INK4c).
Journal of biomolecular structure & dynamics 2010;27(4):521-40.
2010: Mark A Ditzler; Michal Otyepka; Jirì Sponer; Nils G Walter
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
Accounts of chemical research 2010;43(1):40-7.
2009: Ivana Besseová; Michal Otyepka; Kamila Réblová; Jirí Sponer
Dependence of A-RNA simulations on the choice of the force field and salt strength.
Physical chemistry chemical physics : PCCP 2009;11(45):10701-11.
2009: Martina Pavlova; Martin Klvana; Zbynek Prokop; Radka Chaloupkova; Pavel Banas; Michal Otyepka; Rebecca C Wade; Masataka Tsuda; Yuji Nagata; Jiri Damborsky
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
Nature chemical biology 2009;5(10):727-33.
2009: Pavel Banás; Petr Jurecka; Nils Walter; Jirí Sponer; Michal Otyepka
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
Methods (San Diego, Calif.) 2009;49(2):202-16.
2009: Martin Kubala; Lenka Grycova; Zdenek Lansky; Petr Sklenovsky; Marika Janovska; Michal Otyepka; Jan Teisinger
Changes in electrostatic surface potential of Na+/K+-ATPase cytoplasmic headpiece induced by cytoplasmic ligand(s) binding.
Biophysical journal 2009;97(6):1756-64.
2009: Lenka Grycova; Petr Sklenovsky; Zdenek Lansky; Marika Janovska; Michal Otyepka; Evzen Amler; Jan Teisinger; Martin Kubala
ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece.
Biochimica et biophysica acta 2009;1788(5):1081-91.
2008: Pavel Banás; Lubomír Rulísek; Veronika Hánosová; Daniel Svozil; Nils Walter; Jirí Sponer; Michal Otyepka
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.
The journal of physical chemistry. B 2008;112(35):11177-87.
2008: Petr Sklenovský; Pavel Banás; Michal Otyepka
Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c.
Journal of molecular modeling 2008;14(8):747-59.
2008: Iveta Bártová; Jaroslav Koca; Michal Otyepka
Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations.
Journal of molecular modeling 2008;14(8):761-8.
2008: Josef Skopalík; Pavel Anzenbacher; Michal Otyepka
Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences.
The journal of physical chemistry. B 2008;112(27):8165-73.
2008: Michal Otyepka; Pavel Banás; Alessandra Magistrato; Paolo Carloni; Jirí Damborský
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods.
Proteins 2008;70(3):707-17.
2008: Iveta Bártová; Jaroslav Koca; Michal Otyepka
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation.
Protein science : a publication of the Protein Society 2008;17(1):22-33.
2007: Martin Petrek; Pavlína Kosinová; Jaroslav Koca; Michal Otyepka
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
Structure (London, England : 1993) 2007;15(11):1357-63.
2007: Tomás Kubar; Petr Jurecka; Jirí Cerný; Jan Rezac; Michal Otyepka; Haydée Valdés; Pavel Hobza
Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.
The journal of physical chemistry. A 2007;111(26):5642-7.
2007: Jan Filip; Radek Zboril; Oldrich Schneeweiss; Josef Zeman; Miroslav Cernik; Petr Kvapil; Michal Otyepka
Environmental applications of chemically pure natural ferrihydrite.
Environmental science & technology 2007;41(12):4367-74.
2007: Michal Otyepka; Josef Skopalík; Eva Anzenbacherová; Pavel Anzenbacher
What common structural features and variations of mammalian P450s are known to date?
Biochimica et biophysica acta 2007;1770(3):376-89.
2007: Jirí Damborský; Martin Petrek; Pavel Banás; Michal Otyepka
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.
Biotechnology journal 2007;2(1):62-7.
2006: Pavel Banás; Michal Otyepka; Petr Jerábek; Martin Petrek; Jirí Damborský
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.
Journal of computer-aided molecular design 2006;20(6):375-83.
2006: Petr Dobes; Michal Otyepka; Miroslav Strnad; Pavel Hobza
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.
Chemistry (Weinheim an der Bergstrasse, Germany) 2006;12(16):4297-304.
2006: Michal Otyepka; Iveta Bártová; Zdenek Kríz; Jaroslav Koca
Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25 and CDK2/cyclin A dynamics.
The Journal of biological chemistry 2006;281(11):7271-81.
2006: Michal Otyepka; Petr Sklenovský; Dominik Horinek; Tomás Kubar; Pavel Hobza
How the stabilization of INK4 tumor suppressor 3D structure evaluated by quantum chemical and molecular mechanics calculations corresponds well with experimental results: interplay of association enthalpy, entropy, and solvation effects.
The journal of physical chemistry. B 2006;110(9):4423-9.
2006: Martin Petrek; Michal Otyepka; Pavel Banás; Pavlína Kosinová; Jaroslav Koca; Jirí Damborský
CAVER: a new tool to explore routes from protein clefts, pockets and cavities.
BMC bioinformatics 2006;7():316.
2005: Iveta Bártová; Michal Otyepka; Zdenek Kríz; Jaroslav Koca
The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK.
Protein science : a publication of the Protein Society 2005;14(2):445-51.
2004: Iveta Bártová; Michal Otyepka; Zdenek Kríz; Jaroslav Koca
Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop.
Protein science : a publication of the Protein Society 2004;13(6):1449-57.
2004: Zdenek Kríz; Michal Otyepka; Iveta Bártová; Jaroslav Koca
Analysis of CDK2 active-site hydration: a method to design new inhibitors.
Proteins 2004;55(2):258-74.
2004: Aaron J Oakley; Martin Klvana; Michal Otyepka; Yuji Nagata; Matthew C J Wilce; Jirí Damborský
Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues.
Biochemistry 2004;43(4):870-8.
2003: Jirí Moravec; Vladimír Krystof; Jan Hanus; Libor Havlícek; Daniela Moravcová; Kvetoslava Fuksová; Marek Kuzma; René Lenobel; Michal Otyepka; Miroslav Strnad
2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors.
Bioorganic & medicinal chemistry letters 2003;13(18):2993-6.
2002: Michal Otyepka; Zdenek Kríz; Jaroslav Koca
Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations.
Journal of biomolecular structure & dynamics 2002;20(2):141-54.
2002: Michal Otyepka; Jirí Damborský
Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains.
Protein science : a publication of the Protein Society 2002;11(5):1206-17.
2000: Michal Otyepka; Vladimír Krystof; Libor Havlícek; V Siglerová; Miroslav Strnad; Jaroslav Koca
Docking-based development of purine-like inhibitors of cyclin-dependent kinase-2.
Journal of medicinal chemistry 2000;43(13):2506-13.