Regional Centre of Advanced Technologies and Materials

Email: michal.otyepka@upol.cz

Adrress: 17. listopadu 12, Olomouc, 771 46, Czech Republic

Phone: (+420) 58 563 4764

Fax: (+420) 585 634 761

Tady bude neviditelný text – prázdná mezera

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

Research activities:

Protein (CDK, Cyt. P450) and RNA molecular dynamics, enzyme and ribozyme catalysis, force field development ( chiOL ), QM/MM methods and their applications in biomolecular research.

Theoretical study on interations of drugs, antioxidants and Cyt. P450 with membranes. Coauthor of software projects for analysis of molecular channels MOLE and CAVER 1.0. Theoretical design of new 2D materials.

International experience:

2000 (May) at EMBL Heidelberg, Germany, group of prof. R. C. Wade
2005 (Nov.) at SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni
2006 (Jun.) at SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni

Publication activities:

Author or co-author of more than 60 papers in international journals. More than 800 citations. LINK TO RESEARCHER ID

Selected best publications in last 8 years

1) 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

2) 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

3) 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.

4) 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.

5) Sponer JE*, Vázquez-Mayagoitia A, Sumpter BG, Leszczynski J, Sponer J*, Otyepka M, Banas P, Fuentes-Cabrera M*; Theoretical Study on the Intermolecular Interactions of Potentially Primordial Base Pair Analogues. Chemistry Eur. J. 16(10), 3057-3065, 2010

6) 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

7) Besseova I, Otyepka M, Reblova K, Sponer* J; Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11, 10701-10711, 2009.

8) 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

9) 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

10) 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

Show publications

Publications

2012

P. Anzenbacher and M. Otyepka, “Hot Topic: Cytochromes P450: Flexibility and Plasticity – Properties
Determining Substrate Preferences,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, pp. 129, 2012.
[Bibtex]

@article ISI:000300417500001,
Author = Anzenbacher, Pavel and Otyepka, Michal,
Title = Hot Topic: Cytochromes P450: Flexibility and Plasticity - Properties
   Determining Substrate Preferences,
Journal = CURRENT DRUG METABOLISM,
Year = 2012,
Volume = 13,
Number = 2,
Pages = 129,
Month = FEB,
ISSN = 1389-2002,
Unique-ID = ISI:000300417500001,

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.
[Bibtex]

@article ISI:000300417500002,
Author = Otyepka, Michal and Berka, Karel and Anzenbacher, Pavel,
Title = Is There a Relationship Between the Substrate Preferences and Structural
   Flexibility of Cytochromes P450?,
Journal = CURRENT DRUG METABOLISM,
Year = 2012,
Volume = 13,
Number = 2,
Pages = 130-142,
Month = FEB,
ISSN = 1389-2002,
Unique-ID = ISI:000300417500002,

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.
[Bibtex]

@article ISI:000300417500006,
Author = Hendrychova, Tereza and Berka, Karel and Navratilova, Veronika and
   Anzenbacher, Pavel and Otyepka, Michal,
Title = Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450
   Probed by Molecular Dynamics Simulations,
Journal = CURRENT DRUG METABOLISM,
Year = 2012,
Volume = 13,
Number = 2,
Pages = 177-189,
Month = FEB,
ISSN = 1389-2002,
Unique-ID = ISI:000300417500006,

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.
[Bibtex]

@article ISI:000297195400014,
Author = Mlynsky, Vojtech and Banas, Pavel and Walter, Nils G. and Sponer, Jiri
   and Otyepka, Michal,
Title = QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility
   of Multiple Competing Reaction Mechanisms,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2011,
Volume = 115,
Number = 47,
Pages = 13911-13924,
Month = DEC 1,
DOI = 10.1021/jp206963g,
ISSN = 1520-6106,
Unique-ID = ISI:000297195400014,

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.
[Bibtex]

@article ISI:000296597300030,
Author = Granatier, Jaroslav and Lazar, Petr and Otyepka, Michal and Hobza, Pavel,
Title = 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 = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2011,
Volume = 7,
Number = 11,
Pages = 3743-3755,
Month = NOV,
DOI = 10.1021/ct200625h,
ISSN = 1549-9618,
Unique-ID = ISI:000296597300030,

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.
[Bibtex]

@article ISI:000295700600015,
Author = Berka, Karel and Hendrychova, Tereza and Anzenbacher, Pavel and Otyepka,
   Michal,
Title = Membrane Position of Ibuprofen Agrees with Suggested Access Path
   Entrance to Cytochrome P450 2C9 Active Site,
Journal = JOURNAL OF PHYSICAL CHEMISTRY A,
Year = 2011,
Volume = 115,
Number = 41,
Pages = 11248-11255,
Month = OCT 20,
DOI = 10.1021/jp204488j,
ISSN = 1089-5639,
Unique-ID = ISI:000295700600015,

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.
[Bibtex]

@article ISI:000295700600019,
Author = Zgarbova, Marie and Jurecka, Petr and Banas, Pavel and Otyepka, Michal
   and Sponer, Judit E. and Leontis, Neocles B. and Zirbel, Craig L. and
   Sponer, Jiri,
Title = 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 = JOURNAL OF PHYSICAL CHEMISTRY A,
Year = 2011,
Volume = 115,
Number = 41,
Pages = 11277-11292,
Month = OCT 20,
DOI = 10.1021/jp204820b,
ISSN = 1089-5639,
Unique-ID = ISI:000295700600019,

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.
[Bibtex]

@article ISI:000294790400024,
Author = Karlicky, Frantisek and Otyepka, Michal,
Title = First Step in the Reaction of Zerovalent Iron with Water,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2011,
Volume = 7,
Number = 9,
Pages = 2876-2885,
Month = SEP,
DOI = 10.1021/ct200372y,
ISSN = 1549-9618,
Unique-ID = ISI:000294790400024,

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.
[Bibtex]

@article ISI:000294790400025,
Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Mladek, Arnost
   and Banas, Pavel and Cheatham, III, Thomas E. and Jurecka, Petr,
Title = Refinement of the Cornell et al. Nucleic Acids Force Field Based on
   Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2011,
Volume = 7,
Number = 9,
Pages = 2886-2902,
Month = SEP,
DOI = 10.1021/ct200162x,
ISSN = 1549-9618,
Unique-ID = ISI:000294790400025,

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.
[Bibtex]

@article ISI:000294790400032,
Author = Sklenovsky, Petr and Florova, Petra and Banas, Pavel and Reblova, Kamila
   and Lankas, Filip and Otyepka, Michal and Sponer, Jiri,
Title = Understanding RNA Flexibility Using Explicit Solvent Simulations: The
   Ribosomal and Group I Intron Reverse Kink-Turn Motifs,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2011,
Volume = 7,
Number = 9,
Pages = 2963-2980,
Month = SEP,
DOI = 10.1021/ct200204t,
ISSN = 1549-9618,
Unique-ID = ISI:000294790400032,

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.
[Bibtex]

@article ISI:000292281200025,
Author = Dobes, Petr and Rezac, Jan and Fanfrlik, Jindrich and Otyepka, Michal
   and Hobza, Pavel,
Title = 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 = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2011,
Volume = 115,
Number = 26,
Pages = 8581-8589,
Month = JUL 7,
DOI = 10.1021/jp202149z,
ISSN = 1520-6106,
Unique-ID = ISI:000292281200025,

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.
[Bibtex]

@article ISI:000288179000005,
Author = Dobes, Petr and Fanfrlik, Jindrich and Rezac, Jan and Otyepka, Michal
   and Hobza, Pavel,
Title = Transferable scoring function based on semiempirical quantum mechanical
   PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors,
Journal = JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
Year = 2011,
Volume = 25,
Number = 3,
Pages = 223-235,
Month = MAR,
DOI = 10.1007/s10822-011-9413-5,
ISSN = 0920-654X,
Unique-ID = ISI:000288179000005,

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.
[Bibtex]

@article ISI:000286482400027,
Author = Berka, Karel and Otyepka, Michal,
Title = Insenstivity to Close Contacts and Inability to Predict Protein
   Foldability,
Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
Year = 2011,
Volume = 28,
Number = 4,
Pages = 633-634,
Month = FEB,
ISSN = 0739-1102,
Unique-ID = ISI:000286482400027,

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.
[Bibtex]

@article ISI:000285277900009,
Author = Hendrychova, Tereza and Anzenbacherova, Eva and Hudecek, Jiri and
   Skopalik, Josef and Lange, Reinhard and Hildebrandt, Peter and Otyepka,
   Michal and Anzenbacher, Pavel,
Title = Flexibility of human cytochrome P450 enzymes: Molecular dynamics and
   spectroscopy reveal important function-related variations,
Journal = BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS,
Year = 2011,
Volume = 1814,
Number = 1, SI,
Pages = 58-68,
Month = JAN,
DOI = 10.1016/j.bbapap.2010.07.017,
ISSN = 1570-9639,
Unique-ID = ISI:000285277900009,

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.
[Bibtex]

@article ISI:000285793900015,
Author = Zboril, Radek and Karlicky, Frantisek and Bourlinos, Athanasios B. and
   Steriotis, Theodore A. and Stubos, Athanasios K. and Georgakilas,
   Vasilios and Safarova, Klara and Jancik, Dalibor and Trapalis, Christos
   and Otyepka, Michal,
Title = Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and its
   Chemical Conversion to Graphene,
Journal = SMALL,
Year = 2010,
Volume = 6,
Number = 24,
Pages = 2885-2891,
Month = DEC 20,
DOI = 10.1002/smll.201001401,
ISSN = 1613-6810,
Unique-ID = ISI:000285793900015,

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.
[Bibtex]

@article ISI:000285217000018,
Author = Mladek, Arnost and Sponer, Judit E. and Jurecka, Petr and Banas, Pavel
   and Otyepka, Michal and Svozil, Daniel and Sponer, Jiri,
Title = Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM
   Calculations and a Comparison with Density Functional Theory and
   Molecular Mechanics,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2010,
Volume = 6,
Number = 12,
Pages = 3817-3835,
Month = DEC,
DOI = 10.1021/ct1004593,
ISSN = 1549-9618,
Unique-ID = ISI:000285217000018,

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.
[Bibtex]

@article ISI:000285217000019,
Author = Banas, Pavel and Hollas, Daniel and Zgarbova, Marie and Jurecka, Petr
   and Orozco, Modesto and Cheatham, III, Thomas E. and Sponer, Jiri and
   Otyepka, Michal,
Title = Performance of Molecular Mechanics Force Fields for RNA Simulations:
   Stability of UUCG and GNRA Hairpins,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2010,
Volume = 6,
Number = 12,
Pages = 3836-3849,
Month = DEC,
DOI = 10.1021/ct100481h,
ISSN = 1549-9618,
Unique-ID = ISI:000285217000019,

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.
[Bibtex]

@article ISI:000283884300026,
Author = Florova, Petra and Sklenovsky, Petr and Banas, Pavel and Otyepka, Michal,
Title = Explicit Water Models Affect the Specific Solvation and Dynamics of
   Unfolded Peptides While the Conformational Behavior and Flexibility of
   Folded Peptides Remain Intact,
Journal = JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
Year = 2010,
Volume = 6,
Number = 11, 3285,
Pages = 3569-3579,
Month = NOV,
DOI = 10.1021/ct1003687,
ISSN = 1549-9618,
Unique-ID = ISI:000283884300026,

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.
[Bibtex]

@article ISI:000279282600015,
Author = Banas, Pavel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
Title = Protonation States of the Key Active Site Residues and Structural
   Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2010,
Volume = 114,
Number = 26,
Pages = 8701-8712,
Month = JUL 8,
DOI = 10.1021/jp9109699,
ISSN = 1520-6106,
Unique-ID = ISI:000279282600015,

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.
[Bibtex]

@article ISI:000279093300010,
Author = Child, Emma S. and Hendrychova, Tereza and McCague, Karen and Futreal,
   Andy and Otyepka, Michal and Mann, David J.,
Title = A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent
   kinase 2 alters the stability of cyclin binding,
Journal = BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH,
Year = 2010,
Volume = 1803,
Number = 7,
Pages = 858-864,
Month = JUL,
DOI = 10.1016/j.bbamcr.2010.04.004,
ISSN = 0167-4889,
Unique-ID = ISI:000279093300010,

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.
[Bibtex]

@article ISI:000277499700047,
Author = Mlynsky, Vojtech and Banas, Pavel and Hollas, Daniel and Reblova, Kamila
   and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
Title = Extensive Molecular Dynamics Simulations Showing That Canonical G8 and
   Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of
   Hairpin Ribozyme,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2010,
Volume = 114,
Number = 19,
Pages = 6642-6652,
Month = MAY 20,
DOI = 10.1021/jp1001258,
ISSN = 1520-6106,
Unique-ID = ISI:000277499700047,

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.
[Bibtex]

@article ISI:000275691500002,
Author = Dvorakova-Hola, Klara and Matuskova, Anna and Kubala, Martin and
   Otyepka, Michal and Kucera, Tomas and Vecer, Jaroslav and Herman, Petr
   and Parkhomenko, Natalya and Kutejova, Eva and Janata, Jiri,
Title = Glycine-Rich Loop of Mitochondrial Processing Peptidase alpha-Subunit Is
   Responsible for Substrate Recognition by a Mechanism Analogous to
   Mitochondrial Receptor Tom20,
Journal = JOURNAL OF MOLECULAR BIOLOGY,
Year = 2010,
Volume = 396,
Number = 5,
Pages = 1197-1210,
Month = MAR 12,
DOI = 10.1016/j.jmb.2009.12.054,
ISSN = 0022-2836,
Unique-ID = ISI:000275691500002,

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.
[Bibtex]

@article ISI:000272599400011,
Author = Sklenovsky, Petr and Otyepka, Michal,
Title = In Silico Structural and Functional Analysis of Fragments of the Ankyrin
   Repeat Protein P18(INK4c),
Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
Year = 2010,
Volume = 27,
Number = 4,
Pages = 521-539,
Month = FEB,
ISSN = 0739-1102,
Unique-ID = ISI:000272599400011,

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.
[Bibtex]

@article ISI:000274289400005,
Author = Ditzler, Mark A. and Otyepka, Michal and Sponer, Jiri and Walter, Nils
   G.,
Title = Molecular Dynamics and Quantum Mechanics of RNA: Conformational and
   Chemical Change We Can Believe In,
Journal = ACCOUNTS OF CHEMICAL RESEARCH,
Year = 2010,
Volume = 43,
Number = 1,
Pages = 40-47,
Month = JAN,
DOI = 10.1021/ar900093g,
ISSN = 0001-4842,
Unique-ID = ISI:000274289400005,

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.
[Bibtex]

@article ISI:000275943400013,
Author = Sponer, Judit E. and Vazquez-Mayagoitia, Alvaro and Sumpter, Bobby G.
   and Leszczynski, Jerzy and Sponer, Jiri and Otyepka, Michal and Banas,
   Pavel and Fuentes-Cabrera, Miguel,
Title = Theoretical Studies on the Intermolecular Interactions of Potentially
   Primordial Base-Pair Analogues,
Journal = CHEMISTRY-A EUROPEAN JOURNAL,
Year = 2010,
Volume = 16,
Number = 10,
Pages = 3057-3065,
DOI = 10.1002/chem.200902068,
ISSN = 0947-6539,
Unique-ID = ISI:000275943400013,

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.
[Bibtex]

@article ISI:000281352300043,
Author = Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Hobza, Pavel
   and Jurecka, Petr,
Title = Large-scale compensation of errors in pairwise-additive empirical force
   fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT
   calculations,
Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
Year = 2010,
Volume = 12,
Number = 35,
Pages = 10476-10493,
DOI = 10.1039/c002656e,
ISSN = 1463-9076,
Unique-ID = ISI:000281352300043,

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.
[Bibtex]

@article ISI:000270039900010,
Author = Pavlova, Martina and Klvana, Martin and Prokop, Zbynek and Chaloupkova,
   Radka and Banas, Pavel and Otyepka, Michal and Wade, Rebecca C. and
   Tsuda, Masataka and Nagata, Yuji and Damborsky, Jiri,
Title = Redesigning dehalogenase access tunnels as a strategy for degrading an
   anthropogenic substrate,
Journal = NATURE CHEMICAL BIOLOGY,
Year = 2009,
Volume = 5,
Number = 10,
Pages = 727-733,
Month = OCT,
DOI = 10.1038/nchembio.205,
ISSN = 1552-4450,
Unique-ID = ISI:000270039900010,

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.
[Bibtex]

@article ISI:000270443600015,
Author = Banas, Pavel and Jurecka, Petr and Walter, Nils G. and Sponer, Jiri and
   Otyepka, Michal,
Title = Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their
   comparison with MD and QM,
Journal = METHODS,
Year = 2009,
Volume = 49,
Number = 2,
Pages = 202-216,
Month = OCT,
DOI = 10.1016/j.ymeth.2009.04.007,
ISSN = 1046-2023,
Unique-ID = ISI:000270443600015,

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.
[Bibtex]

@article ISI:000270380800027,
Author = Kubala, Martin and Grycova, Lenka and Lansky, Zdenek and Sklenovsky,
   Petr and Janovska, Marika and Otyepka, Michal and Teisinger, Jan,
Title = Changes in Electrostatic Surface Potential of Na(+)/K(+)-ATPase
   Cytoplasmic Headpiece Induced by Cytoplasmic Ligand(s) Binding,
Journal = BIOPHYSICAL JOURNAL,
Year = 2009,
Volume = 97,
Number = 6,
Pages = 1756-1764,
Month = SEP 16,
DOI = 10.1016/j.bpj.2009.07.002,
ISSN = 0006-3495,
Unique-ID = ISI:000270380800027,

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, pp. 26, 2009.
[Bibtex]

@article ISI:000267069900070,
Author = Anzenbacher, P. and Anzenbacherova, E. and Hendrychova, T. and Otyepka,
   M. and Hudecek, J. and Hildebrandt, P. and Lange, R.,
Title = Flexibility and plasticity of the structures of cytochromes P450 as a
   property determining their function,
Journal = FEBS JOURNAL,
Year = 2009,
Volume = 276,
Pages = 26,
Month = JUL,
Note = 34th Congress of the Federation-of-European-Biochemical-Societies,
   Prague, CZECH REPUBLIC, JUL 04-09, 2009,
Organization = Federat European Biochem Soc,
ISSN = 1742-464X,
Unique-ID = ISI:000267069900070,

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, pp. 50, 2009.
[Bibtex]

@article ISI:000266300700062,
Author = Banas, Pavel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
Title = Structural Insight into RNA Catalysis Revealed by Molecular Dynamics
   Simulations and QM/MM Calculation,
Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
Year = 2009,
Volume = 26,
Number = 6,
Pages = 50,
Month = JUN,
ISSN = 0739-1102,
Unique-ID = ISI:000266300700062,

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.
[Bibtex]

@article ISI:000266190600019,
Author = Grycova, Lenka and Sklenovsk, Petr and Lansky, Zdenek and Janovska,
   Marika and Otyepka, Michal and Amler, Evzen and Teisinger, Jan and
   Kubala, Martin,
Title = ATP and magnesium drive conformational changes of the Na(+)/K(+)-ATPase
   cytoplasmic headpiece,
Journal = BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES,
Year = 2009,
Volume = 1788,
Number = 5,
Pages = 1081-1091,
Month = MAY,
DOI = 10.1016/j.bbamem.2009.02.004,
ISSN = 0005-2736,
Unique-ID = ISI:000266190600019,

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.
[Bibtex]

@article ISI:000271907200016,
Author = Besseova, Ivana and Otyepka, Michal and Reblova, Kamila and Sponer, Jiri,
Title = Dependence of A-RNA simulations on the choice of the force field and
   salt strength,
Journal = PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
Year = 2009,
Volume = 11,
Number = 45,
Pages = 10701-10711,
DOI = 10.1039/b911169g,
ISSN = 1463-9076,
Unique-ID = ISI:000271907200016,

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.
[Bibtex]

@article ISI:000258800300054,
Author = Banas, Pavel and Rulisek, Lubomir and Hanosova, Veronika and Svozil,
   Daniel and Walter, Nils G. and Sponer, Jiri and Otyepka, Michal,
Title = General base catalysis for cleavage by the active-site cytosine of the
   hepatitis delta virus ribozyme: QM/MM calculations establish chemical
   feasibility,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2008,
Volume = 112,
Number = 35,
Pages = 11177-11187,
Month = SEP 4,
DOI = 10.1021/jp802592z,
ISSN = 1520-6106,
Unique-ID = ISI:000258800300054,

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.
[Bibtex]

@article ISI:000257330700012,
Author = Sklenovsky, Petr and Banas, Pavel and Otyepka, Michal,
Title = Two C-terminal ankyrin repeats form the minimal stable unit of the
   ankyrin repeat protein p18(INK4c),
Journal = JOURNAL OF MOLECULAR MODELING,
Year = 2008,
Volume = 14,
Number = 8,
Pages = 747-759,
Month = AUG,
DOI = 10.1007/s00894-008-0300-5,
ISSN = 1610-2940,
Unique-ID = ISI:000257330700012,

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.
[Bibtex]

@article ISI:000257330700013,
Author = Bartova, Iveta and Koca, Jaroslav and Otyepka, Michal,
Title = Regulatory phosphorylation of cyclin-dependent kinase 2: insights from
   molecular dynamics simulations,
Journal = JOURNAL OF MOLECULAR MODELING,
Year = 2008,
Volume = 14,
Number = 8,
Pages = 761-768,
Month = AUG,
DOI = 10.1007/s00894-008-0312-1,
ISSN = 1610-2940,
Unique-ID = ISI:000257330700013,

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.
[Bibtex]

@article ISI:000257335200028,
Author = Skopalik, Josef and Anzenbacher, Pavel and Otyepka, Michal,
Title = Flexibility of human cytochromes P450: Molecular dynamics reveals
   differences between CYPs 3A4, 2C9, and 2A6, which correlate with their
   substrate preferences,
Journal = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2008,
Volume = 112,
Number = 27,
Pages = 8165-8173,
Month = JUL 10,
DOI = 10.1021/jp800311c,
ISSN = 1520-6106,
Unique-ID = ISI:000257335200028,

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, pp. 447, 2008.
[Bibtex]

@article ISI:000256633301588,
Author = Dzubak, P. and Sarek, J. and Anzenbacher, P. and Masek, V. and Novak, P.
   and Havlicek, V. and Otyepka, M. and Vydra, D. and Hajduch, M.,
Title = Betulinine JS8 induces apoptosis in tumor cells by mitochondrial
   disruption via specific non-covalent interactions with cytochrome c,
Journal = FEBS JOURNAL,
Year = 2008,
Volume = 275,
Number = 1,
Pages = 447,
Month = JUN,
Note = Joint Conference of the 33rd FEBS Congress/11th IUBMB Conference,
   Athens, GREECE, JUN 28-JUL 03, 2008,
ISSN = 1742-464X,
Unique-ID = ISI:000256633301588,

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.
[Bibtex]

@article ISI:000252836300009,
Author = Otyepka, Michal and Banas, Pavel and Magistrato, Alessandra and Carloni,
   Paolo and Damborsky, Jiri,
Title = Second step of hydrolytic dehalogenation in haloalkane dehalogenase
   investigated by QM/MM methods,
Journal = PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
Year = 2008,
Volume = 70,
Number = 3,
Pages = 707-717,
Month = FEB 15,
DOI = 10.1002/prot.21523,
ISSN = 0887-3585,
Unique-ID = ISI:000252836300009,

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.
[Bibtex]

@article ISI:000254379100008,
Author = Anzenbacher, Pavel and Anzenbacherova, Eva and Lange, Reinhard and
   Skopalik, Josef and Otyepka, Michal,
Title = Active sites of cytochromes P450: What are they like?,
Journal = ACTA CHIMICA SLOVENICA,
Year = 2008,
Volume = 55,
Number = 1,
Pages = 63-66,
ISSN = 1318-0207,
Unique-ID = ISI:000254379100008,

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.
[Bibtex]

@article ISI:000251834500004,
Author = Bartova, Iveta and Koca, Jaroslav and Otyepka, Michal,
Title = Functional flexibility of human cyclin-dependent kinase-2 and its
   evolutionary conservation,
Journal = PROTEIN SCIENCE,
Year = 2008,
Volume = 17,
Number = 1,
Pages = 22-33,
Month = JAN,
DOI = 10.1110/ps.072951208,
ISSN = 0961-8368,
Unique-ID = ISI:000251834500004,

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.
[Bibtex]

@article ISI:000251023400007,
Author = Petrek, Martin and Kosinova, Pavlina and Koca, Jaroslav and Otyepka,
   Michal,
Title = MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and
   tunnels,
Journal = STRUCTURE,
Year = 2007,
Volume = 15,
Number = 11,
Pages = 1357-1363,
Month = NOV,
DOI = 10.1016/j.str.2007.10.007,
ISSN = 0969-2126,
Unique-ID = ISI:000251023400007,

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, pp. 127, 2007.
[Bibtex]

@article ISI:000253283800335,
Author = Kubala, M. and Grycova, L. and Lansky, Z. and Otyepka, M. and
   Sklenovsky, P. and Teisinger, J.,
Title = Conformational changes of the cytoplasmic part of Na+/K+-ATPase induced
   by the ligand binding,
Journal = FEBS JOURNAL,
Year = 2007,
Volume = 274,
Number = 1,
Pages = 127,
Month = JUL,
Note = 32nd Congress of the Federation-of-European-Biochemical-Societies
   (FEBS), Vienna, AUSTRIA, JUL 07-12, 2007,
Organization = Federat European Biochem Soc,
ISSN = 1742-464X,
Unique-ID = ISI:000253283800335,

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.
[Bibtex]

@article ISI:000247187600026,
Author = Filip, Jan and Zboril, Radek and Schneeweiss, Oldrich and Zeman, Josef
   and Cernik, Miroslav and Kvapil, Petr and Otyepka, Michal,
Title = Environmental applications of chemically pure natural ferrihydrite,
Journal = ENVIRONMENTAL SCIENCE \& TECHNOLOGY,
Year = 2007,
Volume = 41,
Number = 12,
Pages = 4367-4374,
Month = JUN 15,
DOI = 10.1021/es062312t,
ISSN = 0013-936X,
Unique-ID = ISI:000247187600026,

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.
[Bibtex]

@article ISI:000244384800006,
Author = Otyepka, Michal and Skopalik, Josef and Anzenbacherova, Eva and
   Anzenbacher, Pavel,
Title = What common structural features and variations of mammalian P450s are
   known to date?,
Journal = BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS,
Year = 2007,
Volume = 1770,
Number = 3,
Pages = 376-389,
Month = MAR,
DOI = 10.1016/j.bbagen.2006.09.013,
ISSN = 0304-4165,
Unique-ID = ISI:000244384800006,

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.
[Bibtex]

@article ISI:000239737800001,
Author = Petrek, Martin and Otyepka, Michal and Banas, Pavel and Kosinova,
   Pavlina and Koca, Jaroslav and Damborsky, Jiri,
Title = CAVER: a new tool to explore routes from protein clefts, pockets and
   cavities,
Journal = BMC BIOINFORMATICS,
Year = 2006,
Volume = 7,
Month = JUN 22,
DOI = 10.1186/1471-2105-7-316,
Article-Number = 316,
ISSN = 1471-2105,
Unique-ID = ISI:000239737800001,

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.
[Bibtex]

@article ISI:000241900000003,
Author = Banas, Pavel and Otyepka, Michal and Jerabek, Petr and Petrek, Martin
   and Damborsky, Jiri,
Title = Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant
   haloalkane dehalogenase revealed by molecular modeling,
Journal = JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
Year = 2006,
Volume = 20,
Number = 6,
Pages = 375-383,
Month = JUN,
DOI = 10.1007/s10822-006-9071-1,
ISSN = 0920-654X,
Unique-ID = ISI:000241900000003,

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.
[Bibtex]

@article ISI:000238032400009,
Author = Dobes, P and Otyepka, M and Strnad, M and Hobza, P,
Title = Interaction energies for the purine inhibitor roscovitine with
   cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT
   and empirical calculations,
Journal = CHEMISTRY-A EUROPEAN JOURNAL,
Year = 2006,
Volume = 12,
Number = 16,
Pages = 4297-4304,
Month = MAY 24,
DOI = 10.1002/chem.200501269,
ISSN = 0947-6539,
Unique-ID = ISI:000238032400009,

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.
[Bibtex]

@article ISI:000236030900045,
Author = Otyepka, M and Bartova, I and Kriz, Z and Koca, J,
Title = Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25
   and CDK2/cyclin A dynamics,
Journal = JOURNAL OF BIOLOGICAL CHEMISTRY,
Year = 2006,
Volume = 281,
Number = 11,
Pages = 7271-7281,
Month = MAR 17,
DOI = 10.1074/jbc.M509699200,
ISSN = 0021-9258,
Unique-ID = ISI:000236030900045,

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.
[Bibtex]

@article ISI:000235944500084,
Author = Otyepka, M and Sklenovsky, P and Horinek, D and Kubar, T and Hobza, P,
Title = 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 = JOURNAL OF PHYSICAL CHEMISTRY B,
Year = 2006,
Volume = 110,
Number = 9,
Pages = 4423-4429,
Month = MAR 9,
DOI = 10.1021/jp056890s,
ISSN = 1520-6106,
Unique-ID = ISI:000235944500084,

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.
[Bibtex]

@article ISI:000226626000019,
Author = Bartova, I and Otyepka, M and Kriz, Z and Koca, J,
Title = 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,
Journal = PROTEIN SCIENCE,
Year = 2005,
Volume = 14,
Number = 2,
Pages = 445-451,
Month = FEB,
DOI = 10.1110/ps.04959705,
ISSN = 0961-8368,
Unique-ID = ISI:000226626000019,

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.
[Bibtex]

@article ISI:000221630900002,
Author = Bartova, I and Otyepka, M and Kriz, Z and Koca, J,
Title = Activation and inhibition of cyclin-dependent kinase-2 by
   phosphorylation; a molecular dynamics study reveals the functional
   importance of the glycine-rich loop,
Journal = PROTEIN SCIENCE,
Year = 2004,
Volume = 13,
Number = 6,
Pages = 1449-1457,
Month = JUN,
DOI = 10.1110/ps.03578504,
ISSN = 0961-8368,
Unique-ID = ISI:000221630900002,

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.
[Bibtex]

@article ISI:000220980600007,
Author = Kriz, Z and Otyepka, M and Bartova, I and Koca, J,
Title = Analysis of CDK2 active-site hydration: A method to design new
   inhibitors,
Journal = PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
Year = 2004,
Volume = 55,
Number = 2,
Pages = 258-274,
Month = MAY 1,
DOI = 10.1002/prot.20026,
ISSN = 0887-3585,
Unique-ID = ISI:000220980600007,

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.
[Bibtex]

@article ISI:000188504800005,
Author = Oakley, AJ and Klvana, M and Otyepka, M and Nagata, Y and Wilce, MCJ and
   Damborsky, J,
Title = Crystal structure of haloalkane dehalogenase LinB from Sphingomonas
   paucimobilis UT26 at 0.95 angstrom resolution: Dynamics of catalytic
   residues,
Journal = BIOCHEMISTRY,
Year = 2004,
Volume = 43,
Number = 4,
Pages = 870-878,
Month = FEB 3,
DOI = 10.1021/bi034748g,
ISSN = 0006-2960,
Unique-ID = ISI:000188504800005,

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.
[Bibtex]

@article ISI:000187446900028,
Author = Pytela, O and Otyepka, M and Kulhanek, J and Otyepkova, E and Nevecna, T,
Title = 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 = JOURNAL OF PHYSICAL CHEMISTRY A,
Year = 2003,
Volume = 107,
Number = 51,
Pages = 11489-11496,
Month = DEC 25,
DOI = 10.1021/jp022664w,
ISSN = 1089-5639,
Unique-ID = ISI:000187446900028,

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.
[Bibtex]

@article ISI:000185221400010,
Author = Moravec, J and Krystof, V and Hanus, J and Havlicek, L and Moravcova, D
   and Fuksova, K and Kuzma, M and Lenobel, R and Otyepka, M and Strnad, M,
Title = 2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors,
Journal = BIOORGANIC \& MEDICINAL CHEMISTRY LETTERS,
Year = 2003,
Volume = 13,
Number = 18,
Pages = 2993-2996,
Month = SEP 15,
DOI = 10.1016/S0960-894X(03)00632-2,
ISSN = 0960-894X,
Unique-ID = ISI:000185221400010,

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. Part 15, pp. 65-74, 2003.
[Bibtex]

@article ISI:000220561700008,
Author = Wiedermannova, I and Otyepka, M and Styskala, J and Slouka, J,
Title = The synthesis of some polycyclic N-H acids with quinoxaline and
   [1,2,4]triazines,
Journal = ARKIVOC,
Year = 2003,
Number = Part 15,
Pages = 65-74,
Unique-ID = ISI:000220561700008,

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.
[Bibtex]

@article ISI:000179043800001,
Author = Otyepka, M and Kriz, Z and Koca, J,
Title = Dynamics and binding modes of free cdk2 and its two complexes with
   inhibitors studied by computer simulations,
Journal = JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS,
Year = 2002,
Volume = 20,
Number = 2,
Pages = 141-154,
Month = OCT,
ISSN = 0739-1102,
Unique-ID = ISI:000179043800001,

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.
[Bibtex]

@article ISI:000175141900021,
Author = Otyepka, M and Damborsky, J,
Title = Functionally relevant motions of haloalkane dehalogenases occur in the
   specificity-modulating cap domains,
Journal = PROTEIN SCIENCE,
Year = 2002,
Volume = 11,
Number = 5,
Pages = 1206-1217,
Month = MAY,
DOI = 10.1110/ps3830102,
ISSN = 0961-8368,
Unique-ID = ISI:000175141900021,

2000

M. Otyepka, V. Krystof, L. Havlicek, V. Siglerova, M. Strnad, and J. Koca, “Docking-based development of purine-like inhibitors of cyclin-dependent
kinase-2,” JOURNAL OF MEDICINAL CHEMISTRY, vol. 43, iss. 13, pp. 2506-2513, 2000.
[Bibtex]

@article ISI:000087924900003,
Author = Otyepka, M and Krystof, V and Havlicek, L and Siglerova, V and Strnad, M
   and Koca, J,
Title = Docking-based development of purine-like inhibitors of cyclin-dependent
   kinase-2,
Journal = JOURNAL OF MEDICINAL CHEMISTRY,
Year = 2000,
Volume = 43,
Number = 13,
Pages = 2506-2513,
Month = JUN 29,
DOI = 10.1021/jm990506w,
ISSN = 0022-2623,
Unique-ID = ISI:000087924900003,

Assoc. Prof. Michal Otyepka, Ph.D.