## Contact:

**Email:** michal.otyepka@upol.cz

**Addrress:** 17. listopadu 12, Olomouc, 771 46, Czech Republic

**Phone:** (+420) 58 563 4764 (4756)

**Fax:** (+420) 585 634 761

## Professional

2004 |
Ph.D. Physical chemistry, Palacký University, Olomouc |

2007 |
Doc. (Associate Prof.), Palacký University, Olomouc |

2008 |
Researcher, Institute of Biophysics (group of prof. Šponer), Brno |

2009 |
Head of the Department of Physical Chemistry, Palacký University, Olomouc |

2010 |
Head of the Workpackage „Carbon nanostructures and biomolecules“ of the project RCPTM, Palacký University, Olomouc |

2012 |
Prof., Palacký University, Olomouc |

## International experience

2000 (May) |
EMBL Heidelberg, Germany, group of prof. R. C. Wade |

2005 (Nov.) |
SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni |

2006 (Jun.) |
SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni |

2011 (Nov.) |
Limoges University, France – ERASMUS, teaching in molecular modeling |

2012 (Nov.) |
Limoges University, France – ERASMUS, teaching in molecular modeling |

**Editorial Board Member – Scientific Reports (Nature PG)**

## Research activities

Physical-chemical properties and reactivity of graphene derivatives and 2D materials, non-covalent interactions to 2D materials.

Interactions of drugs, antioxidants, and cytochrome P450 with biomembranes. Coauthor of software projects for analysis of molecular channels MOLE and CAVER 1.0.

Molecular dynamics of biomolecules and complex molecular systems, force field development, QM/MM methods and their applications in biomolecular research.

## Publication activities

Author or co-author of more than 150 papers in international journals and three book chapters. More than 4000 citations; H-index 33.

## Selected Grants

**ERC** – Consolidator, 2D-Chemistry, 2016-2021

**GACR** – Center of Excellence: Controlling Structure and Function of Biomolecules at the Molecular Scale: Theory Meets Experiment (co-PI), 2012-2018

**GACR** – Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach (co-PI), 2012-2016

**NIH** – Unraveling folding and mechanism of a small model ribozyme (co-PI; PI prof. N. G. Walter, University of Michigan, USA), 2011-2015

**GACR** – Biochemistry on the Crossroad from in silico to in vitro (PI), 2009-2012 (12 mil. CZK)

**GACR** – Structural Determinants of Substrate Specificity of Human Cytochromes P450 (PI), 2009-2012 (3 mil. CZK)

**LC512** – Research Center for Biomolecules and Complex Molecular Systems (co-PI), 2005-2011 (3 mil. CZK)

## Supervised Ph.D. Students

- Pavel Banáš (2005-2009)
- Petr Sklenovský (2008-2011)
- Petra Florová (2007-2011)
- Tereza Hendrychová (2008-2012)
- Vojtěch Mlýnský (2009-2014)
- Markéta Paloncýová (2012-)
- Veronika Navrátilová (2014-)

## Selected publications

### Graphene and Graphene Derivatives

Zboril R, Karlický F, Bourlinos* AB, Steriotis TA, Stubos AK, Georgakilas V, Safarova K, Jancik D, Trapalis C, **Otyepka* M**: Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene. Small, 6 (24), 2010

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) to Plane-Wave DFT Calculations. J. Chem. Theor. Comput., 7(11), 3743-3755, 2011

Georgakilas V, **Otyepka M**, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zboril* R, Kim* KS; Functionalization of Graphene; Covalent and Non-Covalent Approaches, Derivatives and Applications. Chem. Rev., 112(11), 6156-6214, 2012

Granatier J, Lazar P, Prucek R, Safarova K, Zboril R, **Otyepka* M**, Hobza* P; Interaction of Graphene and Arenes with Noble Metals. J. Phys. Chem. C, 116(26), 14151-14162, 2012

Karlicky F*, Zboril 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

Lazar P, Zhang S, Safarova K, Li Q, Froning JP, Granatier J, Hobza P, Zboril 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

Lazar P, Karlicky F, Jurecka P, Kocman M, Otyepkova E, Safarova K, **Otyepka M**: Adsorption of Small Organic Molecules on Graphene. J. Am. Chem. Soc., 135(16), 6372–6377, 2013

Karlicky F, Datta K K R, **Otyepka M***, Zboril R*: Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives. ACS Nano, 7(8), 6434-6464, 2013

Karlicky F* and **Otyepka M***: Band Gap and Optical Spectra of Chlorographene, Fluorographene and Graphane from G0W0, GW0 and GW Calculations on Top of PBE and HSE06 Orbitals. (with Cover Art) J. Chem. Theory Comput., 9 (9),4155-4164 , 2013

### Reactivity of (nano) zero-valent iron (nZVI)

Karlický* F, **Otyepka* M**; The First Step in the Reaction of Zerovalent Iron with Water. J. Chem. Theory Comput., 7 (9), 2876-2885, 2011

Lazar P, **Otyepka* M**: Dissociation of Water on Iron Surfaces: Generalized Gradient Functional and Range-Separated Hybrid Functional Study. J. Phys. Chem. C, 116 (48), 25470–-25477, 2012

### Molecular dynamics of RNA

Ditzler M, **Otyepka M**, Sponer* J, Walter* N; Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Acc. Chem. Res., 43(1), 40-47, 2010

Banas P, Hollas D, Zgarbova M, Jurecka P, Orozco M, Cheatham T, Sponer* J, **Otyepka* M**: Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theor. Comput, 6 (12), 3836-3849, 2010.

Banas P, Walter NG, Sponer* J, **Otyepka*** **M**: Protonation States of the Key Active Site Residues and Structural Dynamics of glmS Riboswitch as Revealed by Molecular Dynamics (with Cover Art) J. Phys. Chem. B, 114 (26), 8701-8712, 2010

Besseova I, Banas P, Kuhrova P, Kosinova P, **Otyepka M**, Sponer* 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

Zgarbova M, **Otyepka M**, Sponer J, Mladek A, Banas P, Cheatham TE, Jurecka* 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

Sponer J, Mladek A, Sponer JE, Svozil D, Zgarbova M, Banas P, Jurecka P, **Otyepka M**; DNA and RNA sugar-phosphate backbone emerges as the key player. Overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14, 15257-15277, 2012

Kuhrova P, Banas P, Best RB, Sponer J, **Otyepka M**: Computer folding of RNA tetraloops? Are we there yet? J. Chem. Theory Comput., 9(4), 2115-2125, 2013

Karlický F, Lazar P, Dubecký M, **Otyepka* M**: The Random Phase Approximation in Surface Chemistry: Water Splitting on Iron. J. Chem. Theory Comput., 9(8), 3670-3676, 2013

### Molecular Dynamics of Proteins

Florova P, Sklenovsky P, Banas 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. Theor. Comp., 6(11), 3569-3579, 2010.

Berka K, Hendrychova 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

**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

Hendrychova T, Anzenbacherova E, Hudecek J, Skopalik 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, 1814 (1), 58-68, 2011

Skopalik 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

### Hybrid QM/MM Calculations

Mlynsky V, Banas P, Walter NG, Sponer 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

Banas P, Jurecka P, Walter NG, Sponer J, **Otyepka* M**; Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. (Invited Review) Methods, 49(2), 202-216, 2009

Banas P, Rulisek L, Hanosova V, Svozil D, Walter N, Sponer* 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

### Simulations of Drug-Membrane Interaction

Paloncyova M, Berka* K, **Otyepka* M**; Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. (with Cover Art) J. Chem. Theory Comput., 8(4), 1200-1211, 2012

Kosinova 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

Paloncyova M, Berka K, **Otyepka* M**: Molecular Insight to Affinities of Drugs and Their Metabolites to Lipid Bilayers. J. Phys. Chem. B, 117(8), 2403-2410, 2013

### Molecular Channels, Tunnels and Pores (MOLE, MOLEonline, CAVER)

Link to MOLEonline 2.0

Sehnal D, Svobodova Varekova R, Berka K, Pravda L, Navratilova V, Banas P, Ionescu CM, **Otyepka* M**, Koca* J: MOLE 2.0: Advanced Approach for Analysis of Biomacromolecular Channels. J. Cheminform., 5, 39, 2013

Berka K, Hanak O, Sehnal D, Banas P, Navratilova V, Jaiswal D, Ionescu CM, Svobodova Varekova R, Koca* J, **Otyepka* M**; MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nuc. Acids Res., 40(W1), W222-W227, 2012

Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, **Otyepka M**, Wade RC, Tsuda M, Nagata Y, Damborsky* J; Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chem. Biol., 5(10), 727-33, 2009

Petrek M, Kosinova P, Koca J, **Otyepka* M**; MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels. Structure 15(11), 1357-1363, 2007

Petrek M, **Otyepka* M**, Banas P, Kosinova P, Koca J, Damborsky***** J; CAVER: A new tool to explore routes from protein clefts, pockets and cavities, BMC Bioinformatics 7:316 2006

### List of publications by years

### 2013

- O. N. Pozharitskaya, A. N. Shikov, M. N. Makarova, S. A. Ivanova, V. M. Kosman, V. G. Makarov, V. Bazgier, K. Berka, M. Otyepka, and J. Ulrichova, “Antiallergic Effects of Pigments Isolated from Green Sea Urchin (Strongylocentrotus droebachiensis) Shells,” PLANTA MEDICA, vol. 79, iss. 18, pp. 1698-1704, 2013.
- J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, and M. Otyepka, “Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment,” BIOPOLYMERS, vol. 99, iss. 12, SI, pp. 978-988, 2013.
- J. Sponer, J. E. Sponer, A. Mladek, P. Banas, P. Jurecka, and M. Otyepka, “How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists,” METHODS, vol. 64, iss. 1, pp. 3-11, 2013.
- K. Berka, M. Paloncyova, P. Anzenbacher, and M. Otyepka, “Behavior of Human Cytochromes P450 on Lipid Membranes,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 117, iss. 39, pp. 11556-11564, 2013.
- M. Dubecky, P. Jurecka, R. Derian, P. Hobza, M. Otyepka, and L. Mitas, “Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, iss. 10, pp. 4287-4292, 2013.
- T. Kucera, M. Otyepka, A. Matuskova, A. Samad, E. Kutejova, and J. Janata, “A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase,” PLOS ONE, vol. 8, iss. 9, 2013.
- L. Lapcik, E. Otyepkova, B. Lapcikova, and M. Otyepka, “Surface energy analysis (SEA) study of hyaluronan powders,” COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS, vol. 436, pp. 1170-1174, 2013.
- D. Sehnal, R. S. Varekova, K. Berka, L. Pravda, V. Navratilova, P. Banas, C. Ionescu, M. Otyepka, and J. Koca, “MOLE 2.0: advanced approach for analysis of biomacromolecular channels,” JOURNAL OF CHEMINFORMATICS, vol. 5, 2013.
- F. Karlicky, K. K. R. Datta, M. Otyepka, and R. Zboril, “Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives,” ACS NANO, vol. 7, iss. 8, pp. 6434-6464, 2013.
- F. Karlicky, P. Lazar, M. Dubecky, and M. Otyepka, “Random Phase Approximation in Surface Chemistry: Water Splitting on Iron,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, iss. 8, pp. 3670-3676, 2013.
- M. Pykal, K. Safarova, K. M. Siskova, P. Jurecka, A. B. Bourlinos, R. Zboril, and M. Otyepka, “Lipid Enhanced Exfoliation for Production of Graphene Nanosheets,” JOURNAL OF PHYSICAL CHEMISTRY C, vol. 117, iss. 22, pp. 11800-11803, 2013.
- P. Podloucka, K. Berka, G. Fabre, M. Paloncyova, J. Duroux, M. Otyepka, and P. Trouillas, “Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 117, iss. 17, pp. 5043-5049, 2013.
- M. Zgarbova, F. Javier Luque, J. Sponer, T. E. Cheatham III, M. Otyepka, and P. Jurecka, “Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, iss. 5, pp. 2339-2354, 2013.
- P. Lazar, F. Karlicky, P. Jurecka, M. Kocman, E. Otyepkova, K. Safarova, and M. Otyepka, “Adsorption of Small Organic Molecules on Graphene,” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 135, iss. 16, pp. 6372-6377, 2013.
- P. Kuehrova, P. Banas, R. B. Best, J. Sponer, and M. Otyepka, “Computer Folding of RNA Tetraloops? Are We There Yet?,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, iss. 4, pp. 2115-2125, 2013.
- J. Granatier, M. Dubecky, P. Lazar, M. Otyepka, and P. Hobza, “Spin-Crossing in an Organometallic Pt-Benzene Complex,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, iss. 3, pp. 1461-1468, 2013.
- M. Paloncyova, K. Berka, and M. Otyepka, “Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 117, iss. 8, pp. 2403-2410, 2013.
- M. Krepl, M. Otyepka, P. Banas, and J. Sponer, “Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 117, iss. 6, pp. 1872-1879, 2013.
- P. Lazar, S. Zhang, K. Safarova, Q. Li, J. P. Froning, J. Granatier, P. Hobza, R. Zboril, F. Besenbacher, M. Dong, and M. Otyepka, “Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions,” ACS NANO, vol. 7, iss. 2, pp. 1646-1651, 2013.
- P. Kuehrova, P. Banas, R. B. Best, J. Sponer, and M. Otyepka, “Computer folding of RNA tetraloops? Are we there yet?,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 31, iss. 1, SI, pp. 25-26, 2013.
- P. Jurecka, M. Zgarbova, F. Javier Luque, J. Sponer, and M. Otyepka, “Deriving force field dihedral angle parameters that account for conformation-dependent solvation effects,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 31, iss. 1, SI, pp. 67-68, 2013.
- M. Zgarbova, M. Otyepka, P. Banas, F. Javier Luque, T. E. Cheatham III, J. Sponer, and P. Jurecka, “Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 31, iss. 1, SI, p. 70, 2013.
- A. Mladek, M. Krepl, D. Svozil, P. Cech, M. Otyepka, P. Banas, M. Zgarbova, P. Jurecka, and J. 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, vol. 15, iss. 19, pp. 7295-7310, 2013.

### 2012

- F. Karlicky, M. Otyepka, and D. Schroeder, “Ligand effects on single-electron transfer of isolated iron atoms in the gaseous complexes [(OC)(m)Fe(OH2)(n)](+) (m, n=0-2, m plus n=1, 2),” INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, vol. 330, pp. 95-99, 2012.
- P. Lazar and M. Otyepka, “Dissociation of Water at Iron Surfaces: Generalized Gradient Functional and Range-Separated Hybrid Functional Study,” JOURNAL OF PHYSICAL CHEMISTRY C, vol. 116, iss. 48, pp. 25470-25477, 2012.
- V. Georgakilas, M. Otyepka, A. B. Bourlinos, V. Chandra, N. Kim, C. K. Kemp, P. Hobza, R. Zboril, and K. S. Kim, “Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications,” CHEMICAL REVIEWS, vol. 112, iss. 11, pp. 6156-6214, 2012.
- P. Banas, P. Sklenovsky, J. E. Wedekind, J. Sponer, and M. Otyepka, “Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, iss. 42, pp. 12721-12734, 2012.
- M. Zgarbova, F. Javier Luque, J. Sponer, M. Otyepka, and P. Jurecka, “A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 8, iss. 9, pp. 3232-3242, 2012.
- I. Besseova, P. Banas, P. Kuehrova, P. Kosinova, M. Otyepka, and J. Sponer, “Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, iss. 33, pp. 9899-9916, 2012.
- A. B. Bourlinos, A. Bakandritsos, N. Liaros, S. Couris, K. Safarova, M. Otyepka, and R. Zboril, “Water dispersible functionalized graphene fluoride with significant nonlinear optical response,” CHEMICAL PHYSICS LETTERS, vol. 543, pp. 101-105, 2012.
- F. Karlicky, R. Zboril, and M. Otyepka, “Band gaps and structural properties of graphene halides and their derivates: A hybrid functional study with localized orbital basis sets,” JOURNAL OF CHEMICAL PHYSICS, vol. 137, iss. 3, 2012.
- J. Granatier, P. Lazar, R. Prucek, K. Safarova, R. Zboril, M. Otyepka, and P. Hobza, “Interaction of Graphene and Arenes with Noble Metals,” JOURNAL OF PHYSICAL CHEMISTRY C, vol. 116, iss. 26, pp. 14151-14162, 2012.
- K. Berka, O. Hanak, D. Sehnal, P. Banas, V. Navratilova, D. Jaiswal, C. Ionescu, R. S. Varekova, J. Koca, and M. Otyepka, “MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels,” NUCLEIC ACIDS RESEARCH, vol. 40, iss. W1, p. W222-W227, 2012.
- P. Banas, A. Mladek, M. Otyepka, M. Zgarbova, P. Jurecka, D. Svozil, F. Lankas, and J. Sponer, “Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 8, iss. 7, pp. 2448-2460, 2012.
- M. Krepl, M. Zgarbova, P. Stadlbauer, M. Otyepka, P. Banas, J. Koca, T. E. Cheatham III, P. Jurecka, and J. Sponer, “Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 8, iss. 7, pp. 2506-2520, 2012.
- K. Berka, E. Anzenbacherova, T. Hendrychova, R. Lange, V. Masek, P. Anzenbacher, and M. Otyepka, “Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site,” JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 110, pp. 46-50, 2012.
- P. Kuehrova, A. De Simone, M. Otyepka, and R. B. Best, “Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign,” BIOPHYSICAL JOURNAL, vol. 102, iss. 8, pp. 1897-1906, 2012.
- M. Paloncyova, K. Berka, and M. Otyepka, “Convergence of Free Energy Profile of Coumarin in Lipid Bilayer,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 8, iss. 4, pp. 1200-1211, 2012.
- P. Kosinova, K. Berka, M. Wykes, M. Otyepka, and P. Trouillas, “Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, iss. 4, pp. 1309-1318, 2012.
- P. Anzenbacher and M. Otyepka, “Hot Topic: Cytochromes P450: Flexibility and Plasticity – Properties Determining Substrate Preferences,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, p. 129, 2012.
- M. Otyepka, K. Berka, and P. Anzenbacher, “Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450?,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, pp. 130-142, 2012.
- T. Hendrychova, K. Berka, V. Navratilova, P. Anzenbacher, and M. Otyepka, “Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, pp. 177-189, 2012.
- K. Sripathi, P. Banas, W. Tay, J. Sponer, M. Otyepka, and N. G. Walter, “Structure-Function Relationships Within the Hepatitis Delta Virus Ribozyme,” BIOPHYSICAL JOURNAL, vol. 102, iss. 3, 1, p. 277A, 2012.
- J. Sponer, A. Mladek, J. E. Sponer, D. Svozil, M. Zgarbova, P. Banas, P. Jurecka, and M. 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, vol. 14, iss. 44, pp. 15257-15277, 2012.

### 2011

- V. Mlynsky, P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 47, pp. 13911-13924, 2011.
- J. Granatier, P. Lazar, M. Otyepka, and P. Hobza, “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,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 11, pp. 3743-3755, 2011.
- K. Berka, T. Hendrychova, P. Anzenbacher, and M. Otyepka, “Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11248-11255, 2011.
- M. Zgarbova, P. Jurecka, P. Banas, M. Otyepka, J. E. Sponer, N. B. Leontis, C. L. Zirbel, and J. 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,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11277-11292, 2011.
- F. Karlicky and M. Otyepka, “First Step in the Reaction of Zerovalent Iron with Water,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2876-2885, 2011.
- M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham III, and P. Jurecka, “Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2886-2902, 2011.
- P. Sklenovsky, P. Florova, P. Banas, K. Reblova, F. Lankas, M. Otyepka, and J. Sponer, “Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 7, iss. 9, pp. 2963-2980, 2011.
- P. Dobes, J. Rezac, J. Fanfrlik, M. Otyepka, and P. 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,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, iss. 26, pp. 8581-8589, 2011.
- P. Dobes, J. Fanfrlik, J. Rezac, M. Otyepka, and P. Hobza, “Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,” JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 25, iss. 3, pp. 223-235, 2011.
- K. Sripathi, P. Banas, J. Sponer, M. Otyepka, and N. Walter, “Structural Landmarks of the Hepatitis Delta Virus (HDV) Ribozyme,” BIOPHYSICAL JOURNAL, vol. 100, iss. 3, 1, p. 236, 2011.
- K. Berka and M. Otyepka, “Insenstivity to Close Contacts and Inability to Predict Protein Foldability,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 28, iss. 4, pp. 633-634, 2011.
- T. Hendrychova, E. Anzenbacherova, J. Hudecek, J. Skopalik, R. Lange, P. Hildebrandt, M. Otyepka, and P. Anzenbacher, “Flexibility of human cytochrome P450 enzymes: Molecular dynamics and spectroscopy reveal important function-related variations,” BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, vol. 1814, iss. 1, SI, pp. 58-68, 2011.

### 2010

- R. Zboril, F. Karlicky, A. B. Bourlinos, T. A. Steriotis, A. K. Stubos, V. Georgakilas, K. Safarova, D. Jancik, C. Trapalis, and M. Otyepka, “Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and its Chemical Conversion to Graphene,” SMALL, vol. 6, iss. 24, pp. 2885-2891, 2010.
- A. Mladek, J. E. Sponer, P. Jurecka, P. Banas, M. Otyepka, D. Svozil, and J. Sponer, “Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3817-3835, 2010.
- P. Banas, D. Hollas, M. Zgarbova, P. Jurecka, M. Orozco, T. E. Cheatham III, J. Sponer, and M. Otyepka, “Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 12, pp. 3836-3849, 2010.
- P. Florova, P. Sklenovsky, P. Banas, and M. Otyepka, “Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 11, 3285, pp. 3569-3579, 2010.
- P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 26, pp. 8701-8712, 2010.
- E. S. Child, T. Hendrychova, K. McCague, A. Futreal, M. Otyepka, and D. 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-MOLECULAR CELL RESEARCH, vol. 1803, iss. 7, pp. 858-864, 2010.
- V. Mlynsky, P. Banas, D. Hollas, K. Reblova, N. G. Walter, J. Sponer, and M. Otyepka, “Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, iss. 19, pp. 6642-6652, 2010.
- K. Dvorakova-Hola, A. Matuskova, M. Kubala, M. Otyepka, T. Kucera, J. Vecer, P. Herman, N. Parkhomenko, E. Kutejova, and J. 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, vol. 396, iss. 5, pp. 1197-1210, 2010.
- P. Sklenovsky and M. Otyepka, “In Silico Structural and Functional Analysis of Fragments of the Ankyrin Repeat Protein P18(INK4c),” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 27, iss. 4, pp. 521-539, 2010.
- M. A. Ditzler, M. Otyepka, J. Sponer, and N. G. Walter, “Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In,” ACCOUNTS OF CHEMICAL RESEARCH, vol. 43, iss. 1, pp. 40-47, 2010.
- J. E. Sponer, A. Vazquez-Mayagoitia, B. G. Sumpter, J. Leszczynski, J. Sponer, M. Otyepka, P. Banas, and M. Fuentes-Cabrera, “Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues,” CHEMISTRY-A EUROPEAN JOURNAL, vol. 16, iss. 10, pp. 3057-3065, 2010.
- M. Zgarbova, M. Otyepka, J. Sponer, P. Hobza, and P. 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, vol. 12, iss. 35, pp. 10476-10493, 2010.

### 2009

- P. Banas, P. Jurecka, N. G. Walter, J. Sponer, and M. Otyepka, “Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM,” METHODS, vol. 49, iss. 2, pp. 202-216, 2009.
- M. Pavlova, M. Klvana, Z. Prokop, R. Chaloupkova, P. Banas, M. Otyepka, R. C. Wade, M. Tsuda, Y. Nagata, and J. Damborsky, “Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate,” NATURE CHEMICAL BIOLOGY, vol. 5, iss. 10, pp. 727-733, 2009.
- M. Kubala, L. Grycova, Z. Lansky, P. Sklenovsky, M. Janovska, M. Otyepka, and J. Teisinger, “Changes in Electrostatic Surface Potential of Na+/K+-ATPase Cytoplasmic Headpiece Induced by Cytoplasmic Ligand(s) Binding,” BIOPHYSICAL JOURNAL, vol. 97, iss. 6, pp. 1756-1764, 2009.
- P. Anzenbacher, E. Anzenbacherova, T. Hendrychova, M. Otyepka, J. Hudecek, P. Hildebrandt, and R. Lange, “Flexibility and plasticity of the structures of cytochromes P450 as a property determining their function,” FEBS JOURNAL, vol. 276, p. 26, 2009.
- P. Banas, N. G. Walter, J. Sponer, and M. Otyepka, “Structural Insight into RNA Catalysis Revealed by Molecular Dynamics Simulations and QM/MM Calculation,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 26, iss. 6, p. 816, 2009.
- L. Grycova, P. Sklenovsk, Z. Lansky, M. Janovska, M. Otyepka, E. Amler, J. Teisinger, and M. Kubala, “ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece,” BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, vol. 1788, iss. 5, pp. 1081-1091, 2009.
- I. Besseova, M. Otyepka, K. Reblova, and J. Sponer, “Dependence of A-RNA simulations on the choice of the force field and salt strength,” PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, iss. 45, pp. 10701-10711, 2009.

### 2008

- P. Banas, L. Rulisek, V. Hanosova, D. Svozil, N. G. Walter, J. Sponer, and M. Otyepka, “General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 35, pp. 11177-11187, 2008.
- P. Sklenovsky, P. Banas, and M. Otyepka, “Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18(INK4c),” JOURNAL OF MOLECULAR MODELING, vol. 14, iss. 8, pp. 747-759, 2008.
- I. Bartova, J. Koca, and M. Otyepka, “Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations,” JOURNAL OF MOLECULAR MODELING, vol. 14, iss. 8, pp. 761-768, 2008.
- J. Skopalik, P. Anzenbacher, and M. Otyepka, “Flexibility of human cytochromes P450: Molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, iss. 27, pp. 8165-8173, 2008.
- P. Dzubak, J. Sarek, P. Anzenbacher, V. Masek, P. Novak, V. Havlicek, M. Otyepka, D. Vydra, and M. Hajduch, “Betulinine JS8 induces apoptosis in tumor cells by mitochondrial disruption via specific non-covalent interactions with cytochrome c,” FEBS JOURNAL, vol. 275, iss. 1, p. 447, 2008.
- M. Otyepka, P. Banas, A. Magistrato, P. Carloni, and J. Damborsky, “Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods,” PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 70, iss. 3, pp. 707-717, 2008.
- P. Anzenbacher, E. Anzenbacherova, R. Lange, J. Skopalik, and M. Otyepka, “Active sites of cytochromes P450: What are they like?,” ACTA CHIMICA SLOVENICA, vol. 55, iss. 1, pp. 63-66, 2008.
- I. Bartova, J. Koca, and M. Otyepka, “Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation,” PROTEIN SCIENCE, vol. 17, iss. 1, pp. 22-33, 2008.

### 2007

- M. Petrek, P. Kosinova, J. Koca, and M. Otyepka, “MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels,” STRUCTURE, vol. 15, iss. 11, pp. 1357-1363, 2007.
- T. Kubar, P. Jurecka, J. Cerny, J. Rezac, M. Otyepka, H. Valdes, and P. Hobza, “Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, iss. 26, pp. 5642-5647, 2007.
- M. Kubala, L. Grycova, Z. Lansky, M. Otyepka, P. Sklenovsky, and J. Teisinger, “Conformational changes of the cytoplasmic part of Na+/K+-ATPase induced by the ligand binding,” FEBS JOURNAL, vol. 274, iss. 1, p. 127, 2007.
- J. Filip, R. Zboril, O. Schneeweiss, J. Zeman, M. Cernik, P. Kvapil, and M. Otyepka, “Environmental applications of chemically pure natural ferrihydrite,” ENVIRONMENTAL SCIENCE & TECHNOLOGY, vol. 41, iss. 12, pp. 4367-4374, 2007.
- M. Otyepka, J. Skopalik, E. Anzenbacherova, and P. Anzenbacher, “What common structural features and variations of mammalian P450s are known to date?,” BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, vol. 1770, iss. 3, pp. 376-389, 2007.

### 2006

- M. Petrek, M. Otyepka, P. Banas, P. Kosinova, J. Koca, and J. Damborsky, “CAVER: a new tool to explore routes from protein clefts, pockets and cavities,” BMC BIOINFORMATICS, vol. 7, 2006.
- P. Banas, M. Otyepka, P. Jerabek, M. Petrek, and J. Damborsky, “Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling,” JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 20, iss. 6, pp. 375-383, 2006.
- P. Dobes, M. Otyepka, M. Strnad, and P. Hobza, “Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT and empirical calculations,” CHEMISTRY-A EUROPEAN JOURNAL, vol. 12, iss. 16, pp. 4297-4304, 2006.
- M. Otyepka, I. Bartova, Z. Kriz, and J. Koca, “Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25 and CDK2/cyclin A dynamics,” JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 281, iss. 11, pp. 7271-7281, 2006.
- M. Otyepka, P. Sklenovsky, D. Horinek, T. Kubar, and P. 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,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, iss. 9, pp. 4423-4429, 2006.

### 2005

- I. Bartova, M. Otyepka, Z. Kriz, and J. 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, vol. 14, iss. 2, pp. 445-451, 2005.

### 2004

- I. Bartova, M. Otyepka, Z. Kriz, and J. 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, vol. 13, iss. 6, pp. 1449-1457, 2004.
- Z. Kriz, M. Otyepka, I. Bartova, and J. Koca, “Analysis of CDK2 active-site hydration: A method to design new inhibitors,” PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 55, iss. 2, pp. 258-274, 2004.
- A. Oakley, M. Klvana, M. Otyepka, Y. Nagata, M. Wilce, and J. Damborsky, “Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 angstrom resolution: Dynamics of catalytic residues,” BIOCHEMISTRY, vol. 43, iss. 4, pp. 870-878, 2004.

### 2003

- O. Pytela, M. Otyepka, J. Kulhanek, E. Otyepkova, and T. Nevecna, “Correlation of dissociation constants of 2-and 2,6-substituted anilines in water by methods based on the similarity principle and quantum-chemistry calculations,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 107, iss. 51, pp. 11489-11496, 2003.
- J. Moravec, V. Krystof, J. Hanus, L. Havlicek, D. Moravcova, K. Fuksova, M. Kuzma, R. Lenobel, M. Otyepka, and M. Strnad, “2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors,” BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, vol. 13, iss. 18, pp. 2993-2996, 2003.
- I. Wiedermannova, M. Otyepka, J. Styskala, and J. Slouka, “The synthesis of some polycyclic N-H acids with quinoxaline and [1,2,4]triazines,” ARKIVOC, iss. 15, pp. 65-74, 2003.

### 2002

- M. Otyepka, Z. Kriz, and J. Koca, “Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 20, iss. 2, pp. 141-154, 2002.
- M. Otyepka and J. Damborsky, “Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains,” PROTEIN SCIENCE, vol. 11, iss. 5, pp. 1206-1217, 2002.