Michal Otyepka

发表

Biomacromolecular Fragments and Patterns

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

Jaroslav Koca, Michal Otyepka, Martin Petrek, 2007, Structure.

Structural Bioinformatics Databases of General Use

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

ChannelsDB: database of biomacromolecular tunnels and pores

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2017, Nucleic Acids Res..

Exponential repulsion improves structural predictability of molecular docking

Karel Berka, Michal Otyepka, Václav Bazgier, 2016, J. Comput. Chem..

Detection and Extraction of Fragments

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

Anatomy of enzyme channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2014, BMC Bioinformatics.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2013, Journal of Cheminformatics.

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Michal Otyepka, Thomas E. Cheatham, Jirí Sponer, 2017, J. Chem. Inf. Model..

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Jaroslav Koca, Michal Otyepka, Jirí Damborský, 2006, BMC Bioinformatics.

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2012, Nucleic Acids Res..

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

Michal Otyepka, Pavel Hobza, Jan Rezác, 2011, J. Comput. Aided Mol. Des..

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2018, Nucleic Acids Res..

Anatomy of enzymatic channels and algorithm for its detection

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2014 .

Random Phase Approximation in Surface Chemistry: Water Splitting on Iron.

Michal Otyepka, František Karlický, Petr Lazar, 2013, Journal of chemical theory and computation.

Structural Bioinformatics Tools for Drug Design

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016, SpringerBriefs in Biochemistry and Molecular Biology.

Structural Bioinformatics Tools for Drug Design: Extraction ofBiologically Relevant Information from Structural Databases

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling

Michal Otyepka, Jirí Damborský, Martin Petrek, 2006, J. Comput. Aided Mol. Des..

Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4

Karel Berka, Michal Otyepka, Veronika Navrátilová, 2015, J. Chem. Inf. Model..

Halogenated graphenes: rapidly growing family of graphene derivatives.

Michal Otyepka, František Karlický, M. Otyepka, 2013, ACS nano.

MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2013 .

Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues.

Yuji Nagata, Michal Otyepka, Jirí Damborský, 2004, Biochemistry.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2014, The journal of physical chemistry letters.

Regulatory Phosphorylations of Cyclin-Dependent Kinase 2: AnInsight from the Molecular Dynamics Simulations

Jaroslav Koča, Michal Otyepka, Iveta Bártová, 2008 .

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.

Jaroslav Koča, Michal Otyepka, Carolina Estarellas, 2015, Biochimica et biophysica acta.

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

Michal Otyepka, Pavel Hobza, Petr Lazar, 2011, Journal of chemical theory and computation.

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Physical chemistry chemical physics : PCCP.

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

Michal Otyepka, Jirí Damborský, Martin Petrek, 2007, Biotechnology journal.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.

Michal Otyepka, Marek Havrila, Jiří Šponer, 2017, Journal of chemical theory and computation.

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

Karel Berka, Michal Otyepka, Markéta Paloncýová, 2012, Journal of chemical theory and computation.

Amphiphilic drug-like molecules accumulate in a membrane below the head group region.

Karel Berka, Michal Otyepka, Russell DeVane, 2014, The journal of physical chemistry. B.

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Methods.

Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-inhibitor complexes involving halogen bonds well, while the empirical potential fails.

Michal Otyepka, Pavel Hobza, Jan Rezác, 2011, The journal of physical chemistry. B.

Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations.

Karel Berka, Michal Otyepka, K. Berka, 2012, Current drug metabolism.

Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

Jaroslav Koča, Michal Otyepka, J. Koča, 2008, Journal of molecular modeling.

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Physical chemistry chemical physics : PCCP.

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

Michal Otyepka, Modesto Orozco, Thomas E. Cheatham, 2010, Journal of chemical theory and computation.

How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes?

Michal Otyepka, Marek Havrila, Petr Jurečka, 2017, Wiley interdisciplinary reviews. RNA.

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Biopolymers.

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Giovanni Bussi, Michal Otyepka, Sandro Bottaro, 2016, Journal of chemical theory and computation.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Biopolymers.

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2012, The journal of physical chemistry. B.

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

Michal Otyepka, Pavel Hobza, Petr Jurecka, 2010, Physical chemistry chemical physics : PCCP.

Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences.

Michal Otyepka, Josef Skopalík, M. Otyepka, 2008, The journal of physical chemistry. B.

Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?

Karel Berka, Michal Otyepka, K. Berka, 2012, Current drug metabolism.

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

Jaroslav Koca, Michal Otyepka, Zdenek Kríz, 2005, Protein science : a publication of the Protein Society.

Functional flexibility of human cyclin‐dependent kinase‐2 and its evolutionary conservation

Jaroslav Koca, Michal Otyepka, J. Koča, 2007, Protein science : a publication of the Protein Society.

In silico pharmacology: Drug membrane partitioning and crossing.

Karel Berka, Pierre Marquet, Michal Otyepka, 2016, Pharmacological research.

Activation and inhibition of cyclin‐dependent kinase‐2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine‐rich loop

Jaroslav Koca, Michal Otyepka, Zdenek Kríz, 2004, Protein science : a publication of the Protein Society.

Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site

Karel Berka, Michal Otyepka, K. Berka, 2011, The journal of physical chemistry. A.

Computer Folding of RNA Tetraloops? Are We There Yet?

Michal Otyepka, Robert B Best, Pavel Banáš, 2013, Journal of chemical theory and computation.

A high efficiency H2S gas sensor material: paper like Fe2O3/graphene nanosheets and structural alignment dependency of device efficiency

Qiang Li, Michal Otyepka, Yudong Huang, 2014 .

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

Michal Otyepka, Pavel Hobza, Vojtěch Spiwok, 2015, Journal of chemical theory and computation.

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Alessandra Magistrato, Michal Otyepka, Jiří Damborský, 2008, Proteins.

Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations.

Michal Otyepka, Peter Hildebrandt, Josef Skopalík, 2011, Biochimica et biophysica acta.

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics.

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Journal of chemical theory and computation.

Dependence of A-RNA simulations on the choice of the force field and salt strength.

Michal Otyepka, K. Réblová, Ivana Beššeová, 2009, Physical chemistry chemical physics : PCCP.

Chapter 6:Molecular Dynamics Simulations of RNA Molecules

Michal Otyepka, Nils G. Walter, Pavel Banáš, 2012 .

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Adrian J Mulholland, Michal Otyepka, Pavel Banáš, 2014, Journal of chemical theory and computation.

What common structural features and variations of mammalian P450s are known to date?

Michal Otyepka, Josef Skopalík, M. Otyepka, 2007, Biochimica et biophysica acta.

Functionally relevant motions of haloalkane dehalogenases occur in the specificity‐modulating cap domains

Michal Otyepka, Jiří Damborský, J. Damborský, 2002, Protein science : a publication of the Protein Society.

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

Michal Otyepka, Martin Lepšík, Jindřich Fanfrlík, 2015, European journal of medicinal chemistry.

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.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2015, The journal of physical chemistry. B.

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Yuji Nagata, Michal Otyepka, Zbynek Prokop, 2009, Nature chemical biology.