prof. RNDr. Michal Otyepka, Ph.D.


E-mail:, Room: 3.032

rid Google scholar ResearchGate orcid

Research interests




International experience


Grants, projects

Supervized Ph.D. students




  1. Bakandritsos A, Chronopoulos DD, Jakubec P, Pykal M, Čépe K, Steriotis T, Kalytchuk S, Petr M, Zbořil R, Otyepka M: High‐Performance Supercapacitors Based on a Zwitterionic Network of Covalently Functionalized Graphene with Iron Tetraaminophthalocyanine. Adv. Funct. Mater., 28(29), 1801111, 2018. (DOI)
  2. Chantemargue B, Di Meo F, Berka K, Nicolas P, Arnion H, Essig M, Marquet P, Otyepka M, Trouillas P: Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms. Pharmacol. Res., 133, 318-327, 2018. (DOI)
  3. Cheong YH, Nasir MZM, Bakandritsos A, Pykal M, Jakubec P, Zbořil R, Otyepka M, Pumera M: Cyanographene and Graphene Acid: The Functional Group of Graphene Derivative Determines the Application in Electrochemical Sensing and Capacitors. ChemElectroChem, ASAP, 2018. (DOI)
  4. de la Torre B, Švec M, Hapala P, Redondo J, Krejčí O, Lo R, Manna D, Sarmah A, Nachtigallová D, Tuček J, Blonski P, Otyepka M, Zbořil R, Hobza P, Jelínek P: Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene. Nat. Commun., 9, 2831 , 2018. (DOI)
  5. Lazar P, Otyepková E, Pykal M, Čépe K, Otyepka M: Role of the puckered anisotropic surface in the surface and adsorption properties of black phosphorus. Nanoscale, 10, 8979-8988, 2018. (DOI)
  6. Li Q, Froning JP, Pykal M, Zhang S, Wang Z, Vondrák M, Banáš P, Čépe K, Jurečka P, Šponer J, Zbořil R, Dong M, Otyepka M: RNA nanopatterning on graphene. 2D Mater, 5, 031006, 2018. (DOI)
  7. Matochová D, Medved M, Aristides B, Steklý T, Zbořil R, Otyepka M: 2D Chemistry - Chemical Control of Graphene Derivatization. J. Phys. Chem. Lett., 9(13), 3580–3585, 2018. (DOI)
  8. Medved M, Zoppellaro G, Ugolotti J, Matochová D, Lazar P, Pospíšil T, Bakandritsos A, Tuček J, Zbořil R, Otyepka M: Reactivity of fluorographene is triggered by point defects: beyond the perfect 2D world. Nanoscale, 10, 4696-4707, 2018. (DOI)
  9. Paloncýová M, Langer M, Otyepka M: Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations. J. Chem. Theory Comput., 14(4), 2076–2083, 2018. (DOI)
  10. Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J: ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res, 46(D1), D399–D405, 2018. (DOI)
  11. Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res, 46(W1), W368–W373, 2018. (DOI)
  12. Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Ley AG, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem. Rev., 118(8), 4177–4338, 2018. (DOI)
  13. Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M: Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem, 183, 117-136, 2018. (DOI)
  14. Tuček J, Blonski P, Malina O, Pumera M, Chua CK, Otyepka M, Zbořil R: Morphology‐Dependent Magnetism in Nanographene: Beyond Nanoribbons. Adv. Funct. Mater., 28(22), 1800592, 2018. (DOI)
  15. Zgarbová M, Jurečka P, Šponer J, Otyepka M: A- to B-DNA Transition in AMBER Force Fields and its Coupling to Sugar Pucker. J. Chem. Theory Comput., 14(1), 319–328, 2018. (DOI)


  1. Bakandritsos A, Pykal M, Blonski P, Jakubec P, Chronopoulos DD, Poláková K, Georgakilas V, Cepe K, Tomanec O, Ranc V, Bourlinos AB, Zbořil R, Otyepka M: Cyanographene and Graphene Acid - Emerging Derivatives Enabling High-Yield and Selective Functionalization of Graphene. ACS Nano, 11(3), 2982–2991, 2017. (DOI)
  2. Bartali R, Otyepka M, Pykal M, Lazar P, Micheli V, Gottardi G, Laidani N: Interaction of the Helium, Hydrogen, Air, Argon, Nitrogen Bubbles with Graphite Surface in Water. ACS Appl. Mater. Interfaces, 9(20), 17517–17525, 2017. (DOI)
  3. Blonski P, Otyepka M: First-principles study of the mechanism of wettability transition of defective graphene. Nanotechnology, 28(6), 064003, 2017. (DOI)
  4. Blonski P, Tuček J, Sofer Z, Mazánek V, Petr M, Pumera M, Otyepka M, Zbořil R: Doping with Graphitic Nitrogen Triggers Ferromagnetism in Graphene. J. Am. Chem. Soc., 139(8), 3171–3180, 2017. (DOI)
  5. Chronopoulos DD, Aristides B, Pykal M, Zbořil R, Otyepka M: Chemistry, properties, and applications of fluorographene. Appl. Mater. Today, 9, 60-70, 2017. (DOI)
  6. Chronopoulos DD, Bakandritsos A, Lazar P, Pykal M, Čépe K, Zbořil R, Otyepka M: High-Yield Alkylation and Arylation of Graphene via Grignard Reaction with Fluorographene. Chem. Mater., 29(3), 926–930, 2017. (DOI)
  7. Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc Václav , Otyepka M, Pino S, Di Mauro E: Nonenzymatic Oligomerization of 3',5' Cyclic CMP Induced by Proton- and UV-Irradiation Hints at a Non-Fastidious Origin of RNA. ChemiBioChem, 18(5), 1535–1543, 2017. (DOI)
  8. Froning JP, Lazar P, Pykal M, Li Q, Dong M, Zbořil R, Otyepka M: Direct mapping of chemical oxidation of individual graphene sheets through dynamic force measurements at the nanoscale. Nanoscale , 9, 119-127, 2017. (DOI)
  9. Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J: Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J. Chem. Theory Comput., 13(8), 3911–3926, 2017. (DOI)
  10. Holá K, Sudolská M, Kalytchuk S, Nachtigallová D, Rogach AL, Otyepka M, Zbořil R: Graphitic Nitrogen Triggers Red Fluorescence in Carbon Dots. ACS Nano, 11(12), 12402–12410, 2017. (DOI)
  11. Islam B, Stadlbauer P, Ley AG, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banáš P, Otyepka M, Šponer J: Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. J. Chem. Theory Comput., 13(6), 2458–2480, 2017. (DOI)
  12. Karlický F, Otyepková E, Lo R, Pitoňák M, Jurečka P, Pykal M, Hobza P, Otyepka M: Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite. J. Chem. Theory Comput., 13(3), 1328–1340, 2017. (DOI)
  13. Lazar P, Martincová J, Otyepka M: Is Single Layer MoS2 Stable in the Air? Chem. Eur. J., 23(53), 13233–13239, 2017. (DOI)
  14. Lazar P, Otyepka M: Role of the edge properties in hydrogen evolution reaction on MoS2. Chem. Eur. J., 23(20), 4863–4869, 2017. (DOI)
  15. Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P: Mapping the Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. J. Phys. Chem. B, 121(48), 10828–10840, 2017. (DOI)
  16. Navrátilová V, Paloncýová M, Berka K, Mise S, Haga Y, Matsumura C, Sakaki T, Inui H, Otyepka M: Molecular Insights into the Role of a Distal F240A Mutation that Alters CYP1A1 Activity towards Persistent Organic Pollutants. Biochim. Biophys. Acta, Gen. Subj., 1861(11), 2852-2860, 2017. (DOI)
  17. Otyepková E, Lazar P, Luxa J, Berka K, Cepe K, Sofer Z, Pumera M, Otyepka M: Surface properties of MoS2 probed by inverse gas chromatography and their impact on electrocatalytic properties. Nanoscale, 9, 19236-19244, 2017. (DOI)
  18. Presolski S, Wang L, Loo AH, Ambrosi A, Lazar P, Ranc V, Otyepka M, Zbořil R, Tomanec O, Ugolotti J, Sofer Z, Pumera M: Functional Nanosheet Synthons by Covalent Modification of Transition-Metal Dichalcogenides. Chem. Mater., 29(5), 2066–2073, 2017. (DOI)
  19. Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M: Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim. Biophys. Acta, Gen. Subj., 1861(5), 1246–1263, 2017. (DOI)
  20. Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017. (DOI)
  21. Sudolská M, Otyepka M: Exact roles of individual chemical forms of nitrogen in the photoluminescent properties of nitrogen-doped carbon dots. Appl. Mater. Today, 7, 190–200, 2017. (DOI)
  22. Tuček J, Holá K, Bourlinos AB, Blonski P, Bakandritsos A, Ugolotti J, Dubecký M, Karlický F, Ranc V, Cepe K, Otyepka M, Zbořil R: Room temperature organic magnets derived from sp3 functionalized graphene. Nat. Commun., 8, 14525 , 2017. (DOI)
  23. Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J. Phys. Chem. B, 121(11), 2420–2433, 2017. (DOI)
  24. Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M: Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57(2), 275–287, 2017. (DOI)


  1. Bazgier V, Berka K, Otyepka M, Banáš P: Exponential repulsion improves structural predictability of molecular docking. J. Comput. Chem., 37(28), 2485–2494, 2016. (DOI)
  2. Billat P, Ossman T, Saint-Marcoux F, Essig M, Rerolle J, Kamar N, Rostaing L, Rostaing L, Kaminski H, Fabre G, Otyepka M, Woillard J, Marquet P, Trouillas P, Nicolas P: Multidrug resistance-associated protein 4 (MRP4) controls ganciclovir intracellular accumulation and contributes to ganciclovir-induced neutropenia in renal transplant patients. Pharmacol. Res., 111, 501–508, 2016. (DOI)
  3. Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P: In Silico Pharmacology: Drug Membrane Partitioning and Crossing. Pharmacol. Res., 111, 471–486, 2016. (DOI)
  4. Fourré I, Di Meo F, Podloucká P, Otyepka M, Trouillas P: Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study. J. Mol. Model., 22(8), 1-14, 2016. (DOI)
  5. Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016. (DOI)
  6. Jayaramulu K, Datta KKR, Rösler C, Petr M, Otyepka M, Zbořil R, Fischer RA: Biomimetic Superhydrophobic/Superoleophilic Highly Fluorinated Graphene Oxide and ZIF-8 Composites for Oil–Water Separation. Angew. Chem. Int. Ed., 55(3), 1178–1182, 2016. (DOI)
  7. Kozák O, Sudolská M, Pramanik G, Cígler P, Otyepka M, Zbořil R: Photoluminescent Carbon Nanostructures. Chem. Mater, 28(12), 4085–4128, 2016. (DOI)
  8. Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J. Chem. Theory Comput., 12(9), 4534–4548, 2016. (DOI)
  9. Lapčík L, Otyepka M, Otyepková E, Lapčíková B, Gabriel R, Gavenda A, Prudilová B: Surface heterogeneity: Information from inverse gas chromatography and application to model pharmaceutical substances. Curr. Opin. Colloid Interface Sci., 24, 64–71, 2016. (DOI)
  10. Navrátilová V, Paloncýová M, Berka K, Otyepka M: Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J. Phys. Chem. B, 120(43), 11205–11213, 2016. (DOI)
  11. Otyepková E, Lazar P, Cepe K, Tomanec O, Otyepka M: Organic adsorbates have higher affinities to fluorographene than to graphene. Appl. Mat. Today, 5, 142–149, 2016. (DOI)
  12. Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M: Role of Enzyme Flexibility in Ligand Access and Egress to Active Site – Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4 J. Chem. Theory Comput., 12(4), 2101–2109, 2016. (DOI)
  13. Pykal M, Jurečka P, Karlický F, Otyepka M: Modelling of graphene functionalization. Phys. Chem. Chem. Phys., 18(48), 6351-6372, 2016. (DOI)
  14. Pykal M, Zbořil R, Otyepka M: Fluorografen – benjamínek v rodině grafenových derivátů. Chem. Listy, 110(5), 335-343, 2016. (DOI)
  15. Sarkar S, Sudolská M, Dubecký M, Reckmeier CJ, Rogach AL, Zbořil R, Otyepka M: Graphitic Nitrogen Doping in Carbon Dots Causes Red-Shifted Absorption. J. Phys. Chem. C, 120(2), 1303–1308, 2016. (DOI)
  16. Scott EE, Wolf CR, Otyepka M, Humphreys SC, Reed JR, Henderson CJ, McLaughlin LA, Paloncýová M, Navrátilová V, Berka K, Anzenbacher P, Dahal UP, Barnaba C, Brozik JA, Jones JP, Estrada DF, Laurence JS, Park JW, Backes WL: The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function. Drug. Metab. Dispos., 44(4), 576-590, 2016. (DOI)
  17. Trouillas P, Sancho-García JC, De Freitas V, Gierschner J, Otyepka M, Dangles O: Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment. Chem. Rev., 116(9), 4937–4982, 2016. (DOI)
  18. Tuček J, Blonski P, Sofer Z, Šimek P, Petr M, Pumera M, Otyepka M, Zbořil R: Sulfur Doping Induces Strong Ferromagnetic Ordering in Graphene: Effect of Concentration and Substitution Mechanism. Adv. Mater., 28(25), 5045–5053, 2016. (DOI)
  19. Urbanová V, Karlický F, Matěj A, Šembera F, Janoušek Z, Perman JA, Ranc V, Čépe K, Michl J, Otyepka M, Zbořil R: Fluorinated graphenes as advanced biosensors - Effect of fluorine coverage on electron transfer properties and adsorption of biomolecules. Nanoscale, 8, 12134-12142, 2016. (DOI)


  1. Dubecký M, Otyepková E, Lazar P, Karlický F, Petr M, Čépe K, Banáš P, Zbořil R, Otyepka M: Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives. J. Phys. Chem. Letters, 6(8), 1430-1434, 2015. (DOI)
  2. Dubecký M, Walter NG, Šponer J, Otyepka M, Banáš P: Chemical Feasibility of the General Acid / Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers, 103(10), 550–562, 2015. (DOI)
  3. Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J: Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim. Biophys. Acta, Gen. Subj., 1850(5), 1072-1090, 2015. (DOI)
  4. Fabre G, Bayach I, Berka K, Paloncýová M, Starok M, Rossi C, Duroux J, Otyepka M, Trouillas P: Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes. Chem. Commun., 51(36), 7713-7716, 2015. (DOI)
  5. Fabre G, Hänchen A, Calliste C, Berka K, Banala S, Otyepka M, Süssmuth RD, Trouillas P: Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane. Bioorgan. Med. Chem., 23(15), 4866-4870, 2015. (DOI)
  6. Georgakilas V, Demeslis A, Ntararas E, Kouloumpis A, Dimos K, Gournis D, Kocman M, Otyepka M, Zbořil R: Hydrophilic Nanotube Supported Graphene-Water Dispersible Carbon Superstructure with Excellent Conductivity. Adv. Funct. Mater., 25(10), 1481-1487, 2015. (DOI)
  7. Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M: Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J. Chem. Theory Comput., 11(8), 3866-3877, 2015. (DOI)
  8. Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences Between Available Variants of the AMBER RNA Force Fields. J. Phys. Chem. B, 119, 15176−15190, 2015. (DOI)
  9. Karlický F, Otyepková E, Banáš P, Lazar P, Kocman M, Otyepka M: Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies. J. Phys. Chem. C., 119(35), 20535-20543, 2015. (DOI)
  10. Kocman M, Jurečka P, Dubecký M, Otyepka M, Cho Y, Kim KS: Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals. Phys. Chem. Chem. Phys., 17(9), 6423-6432, 2015. (DOI)
  11. Krepl M, Havrila M, Stadlbauer P, Banáš P, Otyepka M, Pasulka J, Štefl R, Šponer J: Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?. J. Chem Theory Comput., 11(3), 1220-1243, 2015. (DOI)
  12. Lapčík L, Lapčíková B, Otyepková E, Otyepka M, Vlček J, Buňka F, Salek RN: Surface energy analysis (SEA) and rheology of powder milk dairy products. Food Chem., 174, 25-30, 2015. (DOI)
  13. Lazar P, Chua CK, Holá K, Zbořil R, Otyepka M, Pumera M: Dichlorocarbene-Functionalized Fluorographene: Synthesis and Reaction Mechanism. Small, 11(31), 3790-3796, 2015. (DOI)
  14. Lazar P, Martincová J, Otyepka M: Structure, dynamical stability, and electronic properties of phases in TaS2 from a high-level quantum mechanical calculation. Phys. Rev. B, 92(22), 224104 , 2015. (DOI)
  15. Lazar P, Otyepka M: Accurate surface energies from first principles. Phys. Rev. B., 91(11), 115402, 2015. (DOI)
  16. Lazar P, Otyepková E, Karlický F, Čépe K, Otyepka M: The surface and structural properties of graphite fluoride. Carbon, 94, 804-809, 2015. (DOI)
  17. Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P: Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with $epsilon$/$zeta$ Force Field Reparametrizations. J. Phys. Chem. B., 119(11), 4220-4229, 2015. (DOI)
  18. Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P: The role of an active site Mg 2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys. Chem. Chem. Phys., 17(1), 670-679, 2015. (DOI)
  19. Navrátilová V, Paloncyová M, Kajšová M, Berka K, Otyepka M: Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J. Chem. Inf. Model., 55(3), 628–635, 2015. (DOI)
  20. Paloncýová M, Vávrová K, Sovová Ž, DeVane R, Otyepka M, Berka K: Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails. J. Phys. Chem. B., 119(30), 9811-9819, 2015. (DOI)
  21. Sovová Ž, Berka K, Otyepka M, Jurečka P: Coarse-Grain Simulations of Skin Ceramide NS with Newly Derived Parameters Clarify Structure of Melted Phase. J. Phys. Chem. B., 119(10), 3988-3998, 2015. (DOI)
  22. Sripathi KN, Banáš P, Réblová K, Šponer J, Otyepka M, Walter NG: Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Phys. Chem. Chem. Phys., 17(8), 5887-5900, 2015. (DOI)
  23. Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J: Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic. Acids Res., 43(20), 9626-9644, 2015. (DOI)
  24. Sudolská M, Dubecký M, Sarkar S, Reckmeier CJ, Zbořil R, Rogach AL, Otyepka M: Nature of Absorption Bands in Oxygen-Functionalized Graphitic Carbon Dots. J. Phys. Chem. C., 119(23), 13369-13373, 2015. (DOI)
  25. Trouillas P, Di Meo F, Gierschner J, Linares M, Sancho-García JC, Otyepka M: Optical properties of wine pigments: theoretical guidelines with new methodological perspectives. Tetrahedron, 71(20), 3079-3088, 2015. (DOI)
  26. Urbanová V, Holá K, Bourlinos AB, Čépe K, Ambrosi A, Loo AH, Pumera M, Karlický F, Otyepka M, Zbořil R: Thiofluorographene-Hydrophilic Graphene Derivative with Semiconducting and Genosensing Properties. Adv. Mater., 27(14), 2305-2310, 2015. (DOI)
  27. Vorlová B, Nachtigallová D, Jirásková-Vaníčková J, Ajani H, Jansa P, Řezáč J, Fanfrlík J, Otyepka M, Hobza P, Konvalinka J, Lepšík M: Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study. Eur. J. Med. Chem., 89, 189-197, 2015. (DOI)
  28. Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P: Refinement of the Sugar-Phosphate Backbone Torsion Beta for the AMBER Force Fields Improves the Description of Z-DNA and B-DNA. J. Chem. Theory Comput., 11(12), 5723–5736, 2015. (DOI)


  1. Chia X, Ambrosi A, Otyepka M, Zbořil R, Pumera M: Fluorographites (CF x ) n Exhibit Improved Heterogeneous Electron-Transfer Rates with Increasing Level of Fluorination: Towards the Sensing of Biomolecules. Chem. Eur. J., 20(22), 6665-6671, 2014. (DOI)
  2. Datta KKR, Kozák O, Ranc V, Havrdová M, Bourlinos AB, Šafářová K, Holá K, Tománková K, Zoppellaro G, Otyepka M, Zbořil R: Quaternized carbon dot-modified graphene oxide for selective cell labelling – controlled nucleus and cytoplasm imaging. Chem. Commun., 50(74), 10782-10785, 2014. (DOI)
  3. Datta KKR, Petala E, Datta KJ, Perman JA, Tuček J, Bartak P, Otyepka M, Zoppellaro G, Zbořil R: NZVI modified magnetic filter paper with high redox and catalytic activities for advanced water treatment technologies. Chem. Commun., 50(99), 15673-15676, 2014. (DOI)
  4. Dubecký M, Derian R, Jurečka P, Mitas L, Hobza P, Otyepka M: Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy. Phys. Chem. Chem. Phys., 16(38), 20915-20923, 2014. (DOI)
  5. Filip J, Karlický F, Marušák Z, Lazar P, Černík M, Otyepka M, Zbořil R: Anaerobic Reaction of Nanoscale Zerovalent Iron with Water: Mechanism and Kinetics. J. Phys. Chem. C, 118(25), 13817-13825, 2014. (DOI)
  6. Holá K, Bourlinos AB, Kozák O, Berka K, Siskova KM, Havrdova M, Tuček J, Šafářová K, Otyepka M, Giannelis EP, Zbořil R: Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO− induced red-shift emission. Carbon, 70, 279-286, 2014. (DOI)
  7. Jiang Z, Li J, Aslan H, Li Q, Li Y, Chen M, Huang Y, Froning JP, Otyepka M, Zbořil R, Besenbacher F, Dong M: A high efficiency H2S gas sensor material: paper like Fe2O3/graphene nanosheets and structural alignment dependency of device efficiency. J. Mater. Chem. A, 2(19), 6714-6717, 2014. (DOI)
  8. Karlický F, Otyepka M: Band gaps and optical spectra from single- and double-layer fluorographene to graphite fluoride: many-body effects and excitonic states. Ann. Phys., 526(9-10), 408-414, 2014. (DOI)
  9. Karlický F, Otyepka M: Challenges in the theoretical description of nanoparticle reactivity: Nano zero-valent iron. Int. J. Quantum Chem., 114(15), 987-992, 2014. (DOI)
  10. Kührová P, Otyepka M, Šponer J, Banáš P: Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations. J. Chem. Theory Comput., 10(1), 401-411, 2014. (DOI)
  11. Lazar P, Granatier J, Klimeš J, Hobza P, Otyepka M: The nature of bonding and electronic properties of graphene and benzene with iridium adatoms. Phys. Chem. Chem. Phys., 16(38), 20818-20827, 2014. (DOI)
  12. Lazar P, Otyepková E, Banáš P, Fargašová A, Šafářová K, Lapčík L, Pechoušek J, Zbořil R, Otyepka M: The nature of high surface energy sites in graphene and graphite. Carbon, 73, 448-453, 2014. (DOI)
  13. Lazar P, Zbořil R, Pumera M, Otyepka M: Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties. Phys. Chem. Chem. Phys., 16(27), 14231-14235, 2014. (DOI)
  14. Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J: Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J. Chem. Theory Comput., 10(1), 463-480, 2014. (DOI)
  15. Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M: Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J. Chem. Theory Comput., 10(4), 1608-1622, 2014. (DOI)
  16. Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M: Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region. J. Phys. Chem. B, 118(4), 1030-1039, 2014. (DOI)
  17. Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M: Rationalization of Reduced Penetration of Drugs through Ceramide Gel Phase Membrane. Langmuir, 30(46), 13942-13948, 2014. (DOI)
  18. Paloncýová M, Fabre G, DeVane RH, Trouillas P, Berka K, Otyepka M: Benchmarking of Force Fields for Molecule–Membrane Interactions. J. Chem. Theory Comput., 10(9), 4143-4151, 2014. (DOI)
  19. Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M: Anatomy of enzyme channels. BMC Bioinf., 15(1), 379, 2014. (DOI)
  20. Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (DOI)
  21. Sripathi KN, Tay WW, Banáš P, Otyepka M, Šponer J, Walter NG: Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA, 20(7), 1112-1128, 2014. (DOI)
  22. Zgarbová M, Otyepka M, Šponer J, Lankaš F, Jurečka P: Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput., 10(8), 3177-3189, 2014. (DOI)


  1. Berka K, Paloncýová M, Anzenbacher P, Otyepka M: Behavior of Human Cytochromes P450 on Lipid Membranes. J. Phys. Chem. B, 117(39), 11556-11564, 2013. (DOI)
  2. Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L: Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J. Chem. Theory Comput., 9(10), 4287-4292, 2013. (DOI)
  3. Granatier J, Dubecký M, Lazar P, Otyepka M, Hobza P: Spin-Crossing in an Organometallic Pt–Benzene Complex. J. Chem. Theory Comput., 9(3), 1461-1468, 2013. (DOI)
  4. Karlický F, Kumara Ramanatha Datta K, Otyepka M, Zbořil R: Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives. ACS Nano, 7(8), 6434-6464, 2013. (DOI)
  5. Karlický F, Lazar P, Dubecký M, Otyepka M: Random Phase Approximation in Surface Chemistry: Water Splitting on Iron. J. Chem. Theory Comput., 9(8), 3670-3676, 2013. (DOI)
  6. Karlický F, Otyepka M: Band Gaps and Optical Spectra of Chlorographene, Fluorographene and Graphane from G 0 W 0 , GW 0 and GW Calculations on Top of PBE and HSE06 Orbitals. J. Chem. Theory Comput., 9(9), 4155-4164, 2013. (DOI)
  7. Krepl M, Otyepka M, Banáš P, Šponer J: Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. J. Phys. Chem. B, 117(6), 1872-1879, 2013. (DOI)
  8. Kučera T, Otyepka M, Matušková A, Samad A, Kutejová E, Janata J: A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase. PLoS ONE, 8(9), e74518, 2013. (DOI)
  9. Kührová P, Banáš P, Best RB, Šponer J, Otyepka M: Computer Folding of RNA Tetraloops? Are We There Yet?. J. Chem. Theory Comput., 9(4), 2115-2125, 2013. (DOI)
  10. Lapčík L, Otyepková E, Lapčíková B, Otyepka M: Surface energy analysis (SEA) study of hyaluronan powders. Colloids Surf., A, 436, 1170-1174, 2013. (DOI)
  11. Lazar P, Karlický F, Jurečka P, Kocman M, Otyepková E, Šafářová K, Otyepka M: Adsorption of Small Organic Molecules on Graphene. J. Am. Chem. Soc., 135(16), 6372-6377, 2013. (DOI)
  12. Lazar P, Zhang S, Šafářová K, Li Q, Froning JP, Granatier J, Hobza P, Zbořil R, Besenbacher F, Dong M, Otyepka M: Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions. ACS Nano, 7(2), 1646-1651, 2013. (DOI)
  13. Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Šponer J: 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. Phys. Chem. Chem. Phys., 15(19), 7295-7310, 2013. (DOI)
  14. Paloncýová M, Berka K, Otyepka M: Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers. J. Phys. Chem. B, 117(8), 2403-2410, 2013. (DOI)
  15. Podloucká P, Berka K, Fabre G, Paloncýová M, Duroux J, Otyepka M, Trouillas P: Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant. J. Phys. Chem. B, 117(17), 5043-5049, 2013. (DOI)
  16. Pozharitskaya O, Shikov A, Makarova M, Ivanova S, Kosman V, Makarov V, Bazgier V, Berka K, Otyepka M, Ulrichová J: Antiallergic Effects of Pigments Isolated from Green Sea Urchin (Strongylocentrotus droebachiensis) Shells. Planta Med., 79(18), 1698-1704, 2013. (DOI)
  17. Pykal M, Šafářová K, Machalová Šišková K, Jurečka P, Bourlinos AB, Zbořil R, Otyepka M: Lipid Enhanced Exfoliation for Production of Graphene Nanosheets. J. Phys. Chem. C, 117(22), 11800-11803, 2013. (DOI)
  18. Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C, Otyepka M, Koča J: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminf., 5(1), 1-39, 2013. (DOI)
  19. Šponer J, Šponer JE, Mládek A, Banáš P, Jurečka P, Otyepka M: How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods, 64(1), 3-11, 2013. (DOI)
  20. Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 99(12), 978–988, 2013. (DOI)
  21. Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput., 9(5), 2339-2354, 2013. (DOI)


  1. Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput., 8(7), 2448-2460, 2012. (DOI)
  2. Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M: Molecular Mechanism of preQ 1 Riboswitch Action: A Molecular Dynamics Study. J. Phys. Chem. B, 116(42), 12721-12734, 2012. (DOI)
  3. Berka K, Anzenbacherová E, Hendrychová T, Lange R, Mašek V, Anzenbacher P, Otyepka M: Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site. J. Inorg. Biochem., 110, 46-50, 2012. (DOI)
  4. Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vařekova R, Koča J, Otyepka M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res., 40(W1), W222-W227, 2012. (DOI)
  5. Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J. Phys. Chem. B, 116(33), 9899-9916, 2012. (DOI)
  6. Bourlinos AB, Bakandritsos A, Liaros N, Couris S, Šafářová K, Otyepka M, Zbořil R: Water dispersible functionalized graphene fluoride with significant nonlinear optical response. Chem. Phys. Lett., 543, 101-105, 2012. (DOI)
  7. Georgakilas V, Otyepka M, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zbořil R, Kim KS: Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications. Chem. Rev., 112(11), 6156-6214, 2012. (DOI)
  8. Granatier J, Lazar P, Prucek R, Šafářová K, Zbořil R, Otyepka M, Hobza P: Interaction of Graphene and Arenes with Noble Metals. J. Phys. Chem. C, 116(26), 14151-14162, 2012. (DOI)
  9. Hendrychová T, Berka K, Navrátilová V, Anzenbacher P, Otyepka M: Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations. Curr. Drug Metab., 13(2), 177-189, 2012. (DOI)
  10. Karlický F, Otyepka M, Schröder D: Ligand effects on single-electron transfer of isolated iron atoms in the gaseous complexes [(OC)mFe(OH2)n]+ (m, n = 0–2, m + n = 1, 2) Int. J. Mass Spectrom., 330-332, 95-99, 2012. (DOI)
  11. Karlický F, Zbořil R, Otyepka M: Band gaps and structural properties of graphene halides and their derivates: A hybrid functional study with localized orbital basis sets. J. Chem. Phys., 137(3), 034709, 2012. (DOI)
  12. Košinová P, Berka K, Wykes M, Otyepka M, Trouillas P: Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition. J. Phys. Chem. B, 116(4), 1309-1318, 2012. (DOI)
  13. Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8(7), 2506-2520, 2012. (DOI)
  14. Kührová P, De Simone A, Otyepka M, Best RB: Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign. Biophys. J., 102(8), 1897-1906, 2012. (DOI)
  15. Lazar P, Otyepka M: Dissociation of Water at Iron Surfaces: Generalized Gradient Functional and Range-Separated Hybrid Functional Study. J. Phys. Chem. C, 116(48), 25470-25477, 2012. (DOI)
  16. Otyepka M, Berka K, Anzenbacher P: Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450? Curr. Drug Metab., 13(2), 130-142, 2012. (DOI)
  17. Paloncýová M, Berka K, Otyepka M: Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J. Chem. Theory Comput., 8(4), 1200-1211, 2012. (DOI)
  18. Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14(44), 15257-15277, 2012. (DOI)
  19. Šponer J, Otyepka M, Banáš P, Réblová K, Walter NG: Chapter 6. Molecular Dynamics Simulations of RNA Molecules. 129-155, 2012. (DOI)
  20. Zgarbová M, Luque FJ, Šponer J, Otyepka M, Jurečka P: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput., 8(9), 3232-3242, 2012. (DOI)


  1. Berka K, Hendrychová T, Anzenbacher P, Otyepka M: Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site. J. Phys. Chem. A, 115(41), 11248-11255, 2011. (DOI)
  2. Berka K, Otyepka M: Insenstivity to Close Contacts and Inability to Predict Protein Foldability. J. Biomol. Struct. Dyn., 28(4), 633-634, 2011. (DOI)
  3. Dobeš P, Fanfrlík J, Řezáč J, Otyepka M, Hobza P: Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J. Comput.-Aided Mol. Des., 25(3), 223-235, 2011. (DOI)
  4. Dobeš P, Řezáč J, Fanfrlík J, Otyepka M, Hobza P: Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails. J. Phys. Chem. B, 115(26), 8581-8589, 2011. (DOI)
  5. Granatier J, Lazar P, Otyepka M, Hobza P: The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J. Chem. Theory Comput., 7(11), 3743-3755, 2011. (DOI)
  6. Hendrychová T, Anzenbacherová E, Hudeček J, Skopalík J, Lange R, Hildebrandt P, Otyepka M, Anzenbacher P: Flexibility of human cytochrome P450 enzymes: Molecular dynamics and spectroscopy reveal important function-related variations. Biochim. Biophys. Acta, Proteins Proteomics, 1814(1), 58-68, 2011. (DOI)
  7. Karlický F, Otyepka M: First Step in the Reaction of Zerovalent Iron with Water. J. Chem. Theory Comput., 7(9), 2876-2885, 2011. (DOI)
  8. Mlýnský V, Banáš P, Walter NG, Šponer J, Otyepka M: QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. J. Phys. Chem. B, 115(47), 13911-13924, 2011. (DOI)
  9. Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J. Chem. Theory Comput., 7(9), 2963-2980, 2011. (DOI)
  10. Zgarbová M, Jurečka P, Banáš P, Otyepka M, Šponer JE, Leontis NB, Zirbel CL, Šponer J: 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. J. Phys. Chem. A, 115(41), 11277-11292, 2011. (DOI)
  11. Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 7(9), 2886-2902, 2011. (DOI)


  1. Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 6(12), 3836-3849, 2010. (DOI)
  2. Banáš P, Walter NG, Šponer J, Otyepka M: Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics. J. Phys. Chem. B, 114(26), 8701-8712, 2010. (DOI)
  3. Child ES, Hendrychová T, McCague K, Futreal A, Otyepka M, Mann DJ: A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding. Biochim. Biophys. Acta, Mol. Cell. Res., 1803(7), 858-864, 2010. (DOI)
  4. Ditzler MA, Otyepka M, Šponer J, Walter NG: Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Acc. Chem. Res., 43(1), 40-47, 2010. (DOI)
  5. Dvořáková-Holá K, Matušková A, Kubala M, Otyepka M, Kučera T, Večeř J, Heřman P, Parkhomenko N, Kutejova E, Janata J: Glycine-Rich Loop of Mitochondrial Processing Peptidase alpha-Subunit Is Responsible for Substrate Recognition by a Mechanism Analogous to Mitochondrial Receptor Tom20. J. Mol. Biol., 396(5), 1197-1210, 2010. (DOI)
  6. Florová P, Sklenovský P, Banáš P, Otyepka M: Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact. J. Chem. Theory Comput., 6(11), 3569-3579, 2010. (DOI)
  7. Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J: Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J. Chem. Theory Comput., 6(12), 3817-3835, 2010. (DOI)
  8. Mlýnský V, Banáš P, Hollas D, Réblová K, Walter NG, Šponer J, Otyepka M: Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H + Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. J. Phys. Chem. B, 114(19), 6642-6652, 2010. (DOI)
  9. Sklenovský P, Otyepka M: In Silico Structural and Functional Analysis of Fragments of the Ankyrin Repeat Protein p18 INK4c. J. Biomol. Struct. Dyn., 27(4), 521-539, 2010. (DOI)
  10. Šponer JE, Vázquez-Mayagoitia Á, Sumpter BG, Leszczynski J, Šponer J, Otyepka M, Banáš P, Fuentes-Cabrera M: Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chem. Eur. J., 16(10), 3057-3065, 2010. (DOI)
  11. Zbořil R, Karlický F, Bourlinos AB, Steriotis TA, Stubos AK, Georgakilas V, Šafářová K, Jančík D, Trapalis C, Otyepka M: Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and its Chemical Conversion to Graphene. Small, 6(24), 2885-2891, 2010. (DOI)
  12. Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)


  1. Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M: Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49(2), 202-216, 2009. (DOI)
  2. Beššeová I, Otyepka M, Réblová K, Šponer J: Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11(45), 10701-10711, 2009. (DOI)
  3. Grycová L, Sklenovský P, Lanský Z, Janovská M, Otyepka M, Amler E, Teisinger J, Kubala M: ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece. Biochim. Biophys. Acta, Biomembr., 1788(5), 1081-1091, 2009. (DOI)
  4. Kubala M, Grycová L, Lansky Z, Sklenovský P, Janovská M, Otyepka M, Teisinger J: Changes in Electrostatic Surface Potential of Na+/K+-ATPase Cytoplasmic Headpiece Induced by Cytoplasmic Ligand(s) Binding. Biophys. J., 97(6), 1756-1764, 2009. (DOI)
  5. Otyepka M, Damborský J: Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Sci., 11(5), 1206-1217, 2009. (DOI)
  6. Pavlová M, Klvana M, Prokop Z, Chaloupková R, Banáš P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborský J: Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat. Chem. Biol., 5(10), 727-733, 2009. (DOI)


  1. Anzenbacher P, Anzenbacherová E, Lange R, Skopalík J, Otyepka M: Active Sites of Cytochromes P450: What are They Like?. Acta Chim. Slov., 55(1), 63-66, 2008. (DOI)
  2. Banáš P, Rulíšek L, Hánošová V, Svozil D, Walter NG, Šponer J, Otyepka M: General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility.. J. Phys. Chem. B, 112(35), 11177-11187, 2008. (DOI)
  3. Bártová I, Koča J, Otyepka M: Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations. J. Mol. Model., 14(8), 761-768, 2008. (DOI)
  4. Sklenovský P, Banáš P, Otyepka M: Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c. J. Mol. Model., 14(8), 747-759, 2008. (DOI)
  5. Skopalík J, Anzenbacher P, Otyepka M: Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences. J. Phys. Chem. B, 112(27), 8165-8173, 2008. (DOI)


  1. Bártová I, Koča J, Otyepka M: Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation. Protein Sci., 17(1), 22-33, 2007. (DOI)
  2. Damborský J, Petřek M, Banáš P, Otyepka M: Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnol. J., 2(1), 62-67, 2007. (DOI)
  3. Filip J, Zbořil R, Schneeweiss O, Zeman J, Černik M, Kvapil P, Otyepka M: Environmental Applications of Chemically Pure Natural Ferrihydrite. Environ. Sci. Technol., 41(12), 4367-4374, 2007. (DOI)
  4. Kubař T, Jurečka P, Černý J, Řezáč J, Otyepka M, Valdés H, Hobza P: Density-Functional, Density-Functional Tight-Binding, and Wave Function Calculations on Biomolecular Systems. J. Phys. Chem. A, 111(26), 5642-5647, 2007. (DOI)
  5. Otyepka M, Banáš P, Magistrato A, Carloni P, Damborský J: Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins Struct. Funct. Bioinf., 70(3), 707-717, 2007. (DOI)
  6. Otyepka M, Skopalík J, Anzenbacherová E, Anzenbacher P: What common structural features and variations of mammalian P450s are known to date?. Biochim. Biophys. Acta, Gen. Subj., 1770(3), 376-389, 2007. (DOI)
  7. Petřek M, Košinová P, Koča J, Otyepka M: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure, 15(11), 1357-1363, 2007. (DOI)


  1. Banáš P, Otyepka M, Jeřábek P, Petřek M, Damborský J: Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput.-Aided Mol. Des., 20(6), 375-383, 2006. (DOI)
  2. Dobeš P, Otyepka M, Strnad M, Hobza P: Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical Calculations. Chem. Eur. J., 12(16), 4297-4304, 2006. (DOI)
  3. Otyepka M, Bártová I, Kříž Z, Koča J: Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/p25 and CDK2/Cyclin A Dynamics. J. Biol. Chem., 281(11), 7271-7281, 2006. (DOI)
  4. Otyepka M, Sklenovský P, Horinek D, Kubař T, Hobza P: 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. J. Phys. Chem. B, 110(9), 4423-4429, 2006. (DOI)
  5. Petřek M, Otyepka M, Banáš P, Košinová P, Koča J, Damborský J: CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinf., 7(1), 316, 2006. (DOI)


  1. Bártová I, Otyepka M, Kříž Z, Koča J: 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 Sci., 14(2), 445-451, 2005. (DOI)


  1. Bártová I, Otyepka M, Kříž Z, Koča J: Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop. Protein Sci., 13(6), 1449-1457, 2004. (DOI)
  2. Kříž Z, Otyepka M, Bártová I, Koča J: Analysis of CDK2 active-site hydration: A method to design new inhibitors. Proteins Struct. Funct. Bioinf., 55(2), 258-274, 2004. (DOI)
  3. Oakley AJ, Klvaňa M, Otyepka M, Nagata Y, Wilce MCJ, Damborský J: Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 AA Resolution: Dynamics of Catalytic Residues. Biochemistry, 43(4), 870-878, 2004. (DOI)


  1. Moravec J, Kryštof V, Hanuš J, Havlı́ček L, Moravcová D, Fuksová K, Kuzma M, Lenobel R, Otyepka M, Strnad M: 2,6,8,9-Tetrasubstituted Purines as New CDK1 Inhibitors. Bioorg. Med. Chem. Lett., 13(18), 2993-2996, 2003. (DOI)
  2. Pytela O, Otyepka M, Kulhánek J, Otyepková E, Nevěčná T: Correlation of Dissociation Constants of 2- and 2,6-Substituted Anilines in Water by Methods Based on the Similarity Principle and Quantum-Chemistry Calculations. J. Phys. Chem. A, 107(51), 11489-11496, 2003. (DOI)
  3. Wiedermannová I, Otyepka M, Stýskala J, Slouka J: The synthesis of some polycyclic N-H acids with quinoxaline and [1,2,4]triazines. Arkivoc, 65-74, 2003. (DOI)


  1. Otyepka M, Kříž Z, Koča J: Dynamics and Binding Modes of Free cdk2 and its Two Complexes with Inhibitors Studied by Computer Simulations. J. Biomol. Struct. Dyn., 20(2), 141-154, 2002. (DOI)


  1. Otyepka M, Kryštof V, Havlíček L, Siglerová V, Strnad M, Koča J: Docking-Based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase-2. J. Med. Chem., 43(13), 2506-2513, 2000. (DOI)