doc. Mgr. Pavel BANÁŠ, Ph.D.

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RCPTM Uhlík

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CATRIN - Technickosprávní úsek

CATRIN

Šlechtitelů 27 - objekt G1 (RCPTM)

3.13

  • vědecký pracovník (RCPTM Uhlík)
  • Ředitel fakultního / univerzitního zaříz (CATRIN - Technickosprávní úsek)

Selected publications
Pravda L., Berka K., Svobodová Vařeková R., Sehnal D., Banáš P., Laskowski RA., Koča J., Otyepka M. Anatomy of enzyme channels. BMC Bioinformatics. 2014. (ČLÁNEK)
Sehnal D., Vařeková R., Berka K., Pravda L., Navrátilová V., Banáš P., Ionescu C., Otyepka M., Koča J. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics. 2013. (ČLÁNEK)
Berka K., Hanák O., Sehnal D., Banáš P., Navrátilová V., Jaiswal D., Ionescu C., Svobodová Vařeková R., Koča J., Otyepka M. MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nucleic Acids Research. 2012. (ČLÁNEK)
ČLÁNEK
Rodrigueiro Flauzino JM., Nalepa M., Chronopoulos D., Šedajová V., Panáček D., Jakubec P., Kührová P., Pykal M., Banáš P., Panáček A., Bakandritsos A., Otyepka M. Click and Detect: Versatile Ampicillin Aptasensor Enabled by Click Chemistry on a Graphene–Alkyne Derivative. Small. 2023.
Kührová P., Mlýnský V., Otyepka M., Šponer J., Banáš P. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. Journal of Chemical Information and Modeling. 2023.
Mlýnský V., Kührová P., Stadlbauer P., Krepl M., Otyepka M., Banáš P., Šponer J. Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. Journal of Chemical Theory and Computation. 2023.
Fröhlking T., Mlýnský V., Janeček M., Kührová P., Krepl M., Banáš P., Šponer J., Bussi G. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of Chemical Theory and Computation. 2022.
Paloncýová M., Pykal M., Kührová P., Banáš P., Šponer J., Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. Small. 2022.
Mlýnský V., Janeček M., Kührová P., Fröhlking T., Otyepka M., Bussi G., Banáš P., Šponer J. Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. Journal of Chemical Theory and Computation. 2022.
Otyepková E., Skladanová K., Pykal M., Blahová Prudilová B., Kašlík J., Čépe K., Banáš P., Lazar P., Otyepka M. Molecular insights from theoretical calculations explain the differences in affinity and diffusion of airborne contaminants on surfaces of hBN and graphene. APPLIED SURFACE SCIENCE. 2021.
Janeček M., Kührová P., Mlýnský V., Otyepka M., Šponer J., Banáš P. W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. Journal of Chemical Theory and Computation. 2021.
Mlýnský V., Kührová P., Kühr T., Otyepka M., Bussi G., Banáš P., Šponer J. Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. Journal of Chemical Theory and Computation. 2020.
Mráziková K., Mlýnský V., Kührová P., Krepl M., Otyepka M., Banáš P. UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations. Journal of Chemical Theory and Computation. 2020.
Cesari A., Bottaro S., Lindorfr-Larsen K., Banáš P., Šponer J., Bussi G. Fitting Corrections to an RNA Force Field Using Experimental Data. Journal of Chemical Theory and Computation. 2019.
Kührová P., Mlýnský V., Zgarbová M., Krepl M., Bussi G., Best RB., Otyepka M., Šponer J., Banáš P. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. Journal of Chemical Theory and Computation. 2019.
Pykal M., Langer M., Blahová Prudilová B., Banáš P., Otyepka M. Ion Interactions across Graphene in Electrolyte Aqueous Solution. Journal of Physical Chemistry C. 2019.
Suddala KC., Price IR., Dandpat SS., Janeček M., Kührová P., Šponer J., Banáš P., Ke A., Walter NG. Local-to-global signal transduction at the core of a Mn2 sensing riboswitch. Nature Communications. 2019.
Stadlbauer P., Kührová P., Vicherek L., Banáš P., Otyepka M., Trantírek L., Šponer J. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. NUCLEIC ACIDS RESEARCH. 2019.
Bonomi M., Bussi G., Camilloni C., Banáš P. Promoting transparency and reproducibility in enhanced molecular simulations. NATURE METHODS. 2019.
Langer R., Zaoralová D., Medveď M., Banáš P., Blonski P., Otyepka M. Variability of C-F Bonds Governs the Formation of Specific Structural Motifs in Fluorinated Graphenes. Journal of Physical Chemistry C. 2019.
LI Q., Froning JP., Pykal M., Zhang S., Wang Z., Vondrák M., Banáš P., Čépe K., Jurečka P., Šponer J., Zbořil R., Dong M., Otyepka M. RNA nanopatterning on graphene. 2D Materials. 2018.
Šponer J., Bussi G., Krepl M., Banáš P., Bottaro S., Cunha RA., Gil-Ley A., Pinamonti G., Poblete S., Jurečka P., Walter NG., Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. CHEMICAL REVIEWS. 2018.
Havrila M., Stadlbauer P., Kührová P., Banáš P., Mergny J., Otyepka M., Šponer J. Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. NUCLEIC ACIDS RESEARCH. 2018.
Islam B., Stadlbauer P., Gil-Ley A., Perez-Hernandez G., Haider S., Neidle S., Bussi G., Banáš P., Otyepka M., Šponer J. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. Journal of Chemical Theory and Computation. 2017.
Šponer J., Bussi G., Stadlbauer P., Kührová P., Banáš P., Islam B., Haider S., Neidle S., Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochimica et Biophysica Acta - General Subjects. 2017.
Šponer J., Krepl M., Banáš P., Kührová P., Zgarbová M., Jurečka P., Havrila M., Otyepka M. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes? Wiley interdisciplinary reviews. RNA. 2017.
Mlýnský V., Kührová P., Jurečka P., Šponer J., Otyepka M., Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. Journal of Physical Chemistry B. 2017.
Zgarbová M., Jurečka P., Banáš P., Havrila M., Šponer J., Otyepka M. Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. Journal of Physical Chemistry B. 2017.
Kührová P., Best RB., Bottaro S., Bussi G., Šponer J., Otyepka M., Banáš P. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. Journal of Chemical Theory and Computation. 2016.
Bazgier V., Berka K., Otyepka M., Banáš P. Exponential Repulsion Improves Structural Predictability of Molecular Docking. Journal of Computational Chemistry. 2016.
Bottaro S., Banáš P., Šponer J., Bussi G. Free Energy Landscape of GAGA and UUCG RNA Tetraloops. Journal of Physical Chemistry Letters. 2016.
Krepl M., Havrila M., Stadlbauer P., Banáš P., Otyepka M., Pasulka J., Štefl R., Šponer J. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation. 2015.
Stadlbauer P., Kührová P., Banáš P., Koča J., Bussi G., Trantírek L., Otyepka M., Šponer J. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. 2015.
Dubecký M., Walter NG., Šponer J., Otyepka M., Banáš P. Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers. 2015.
Haldar S., Kührová P., Banáš P., Spiwok V., Šponer J., Hobza P., Otyepka M. Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. Journal of Chemical Theory and Computation. 2015.
Haldar S., Kührová P., Banáš P., Spiwok V., Šponer J., Hobza P., Otyepka M. Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. Journal of Chemical Theory and Computation. 2015.
Karlický F., Otyepková E., Banáš P., Lazar P., Kocman M., Otyepka M. Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies. Journal of Physical Chemistry Part C: Nanomaterials and Interfaces. 2015.
Estarellas C., Otyepka M., Koča J., Banáš P., Krepl M., Šponer J. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochimica et Biophysica Acta - General Subjects. 2015.
Mlýnský V., Kührová P., Zgarbová M., Jurečka P., Walter NG., Otyepka M., Šponer J., Banáš P. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations. Journal of Physical Chemistry B. 2015.
Dubecký M., Otyepková E., Lazar P., Karlický F., Petr M., Čépe K., Banáš P., Zbořil R., Otyepka M. Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives. Journal of Physical Chemistry Letters. 2015.
Mlýnský V., Walter NG., Šponer J., Otyepka M., Banáš P. The role of an active site Mg2 in HDV ribozyme self-cleavage: insights from QM/MM calculations. Physical Chemistry Chemical Physics. 2015.
Sripathi KN., Banáš P., Reblova K., Šponer J., Otyepka M., Walter NG. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Physical Chemistry Chemical Physics. 2015.
Kührová P., Otyepka M., Šponer J., Banáš P. Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations. Journal of Chemical Theory and Computation. 2014.
Mlýnský V., Banáš P., Šponer J., van der Kamp M., Mulholland A., Otyepka M. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. Journal of Chemical Theory and Computation. 2014.
Sripathi K., Tay W., Banáš P., Otyepka M., Šponer J., Walter N. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA-A Publication of the RNA Society. 2014.
Mládek A., Banáš P., Jurečka P., Otyepka M., Zgarbová M., Šponer J. Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. Journal of Chemical Theory and Computation. 2014.
Šponer J., Banáš P., Jurečka P., Zgarbová M., Kührová P., Havrila M., Krepl M., Stadlbauer P., Otyepka M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. Journal of Physical Chemistry Letters. 2014.
Lazar P., Otyepková E., Banáš P., Fargašová A., Čépe K., Lapčík L., Pechoušek J., Zbořil R., Otyepka M. The nature of high surface energy sites in graphene and graphite. Carbon. 2014.
Mládek A., Krepl M., Svozil D., Cech P., Otyepka M., Banáš P., Zgarbová M., Jurečka P., Šponer J. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Physical Chemistry Chemical Physics. 2013.
Kührová P., Banáš P., Best RB., Šponer J., Otyepka M. Computer Folding of RNA Tetraloops? Are We There Yet? Journal of Chemical Theory and Computation. 2013.
Šponer J., Šponer JE., Mládek A., Banáš P., Jurečka P., Otyepka M. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods. 2013.
Šponer J., Šponer JE., Mládek A., Jurečka P., Banáš P., Otyepka M. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. Biopolymers. 2013.
Banáš P., Mládek A., Otyepka M., Zgarbová M., Jurečka P., Svozil D., Lankaš F., Šponer J. Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. Journal of Chemical Theory and Computation. 2012.
Banáš P., Sklenovský P., Wedekind J., Šponer J., Otyepka M. Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study. Journal of Physical Chemistry B. 2012.
Krepl M., Zgarbová M., Stadlbauer P., Otyepka M., Banáš P., Koča J., Cheatham TE., Jurečka P., Šponer J. Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. Journal of Chemical Theory and Computation. 2012.
Beššeová I., Banáš P., Kührová P., Košinová P., Otyepka M., Šponer J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. Journal of Physical Chemistry B. 2012.
Šponer J., Mládek A., Šponerová JE., Svozil D., Zgarbová M., Banáš P., Jurečka P., Otyepka M. The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Physical Chemistry Chemical Physics. 2012.
ZGARBOVÁ M., JUREČKA P., BANÁŠ P., OTYEPKA M., Šponer JE., Leontis NB., Zirbel CL., Šponer J. Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. Journal of Physical Chemistry A. 2011.
MLÝNSKÝ V., BANÁŠ P., Walter NG., Šponer J., OTYEPKA M. QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. Journal of Physical Chemistry B. 2011.
ZGARBOVÁ M., OTYEPKA M., Šponer J., Mládek A., BANÁŠ P., Cheatham TEI., JUREČKA P. 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. 2011.
SKLENOVSKÝ P., FLOROVÁ P., BANÁŠ P., RÉBLOVÁ K., LANKAŠ F., OTYEPKA M., ŠPONER J. Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. Journal of Chemical Theory and Computation. 2011.
Mládek A., Šponer JE., Jurečka P., Banáš P., Otyepka M., Svozil D., Šponer J. Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. Journal of Chemical Theory and Computation. 2010.
Mlýnský V., Banáš P., Hollas D., Réblová K., Walter NG., Šponer J., Otyepka M. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. Journal of Physical Chemistry B. 2010.
Banáš P., Hollas D., Zgarbová M., Jurečka P., Orozco M., Cheatham Iii TE., Šponer J., Otyepka M. Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA Hairpins. Journal of Chemical Theory and Computation. 2010.
Banáš P., Walter NG., Šponer J., Otyepka M. Protonation states of the key active site residues and structural dynamics of glmS riboswitch as reveled by molecular dynamics. Journal of Physical Chemistry B. 2010.
Šponer JE., Vazquez-Mayagoita A., Sumpter BG., Leszczynski J., Šponer J., Otyepka M., Banáš P., Fuentes-Cabrera M. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chemistry: A European Journal. 2010.
Pavlová M., Klvaňa M., Prokop Z., Chaloupková R., Banáš P., Otyepka M., Wade R., Tsuda M., Nagata Y., Damborský J. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology. 2009.
Banáš P., Jurečka P., Walter N., Šponer J., Otyepka M. Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods. 2009.
Banáš P., Rulíšek L., Hánošová V., Svozil D., Walter NG., Šponer J., Otyepka M. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. Journal of Physical Chemistry B. 2008.
Otyepka M., Banáš P., Magistrato A., Carloni P., Damborský J. Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins: structure, function, and bioinformatics. 2008.
Sklenovský P., Banáš P., Otyepka M. Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c. Journal of Molecular Modeling. 2008.
Damborský J., Petřek M., Banáš P., Otyepka M. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnology Journal. 2007.
Filipová R., Banáš P., Otyepka M., Nevěčná T., Kvítek L. Není důležité vyhrát, ale stát se vědcem. ChemZi. 2007.
Banáš P., Otyepka M., Rulíšek L., Svozil D., Šponer J. Reaction mechanism of hepatitis delta virus ribosyme self-cleavage reaction. ChemZi. 2007.
Petřek M., Otyepka M., Banáš P., Košinová P., Koča J., Damborský J. CAVER: a new tool to explore routes from protein clefts, pockets. BMC Bioinformatics. 2006.
Banáš P., Otyepka M., Jeřábek P., Petřek M., Damborský J. Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. Journal of Computer-Aided Molecular Design. 2006.
Petřek M., Otyepka M., Banáš P., Damborský J. Computational analysis of enzyme active site routes anatomy. Materials Structure in Chemistry, Biology, Physics and Technology. 2005.
PŘÍSPĚVEK VE SBORNÍKU
Banáš P., Petřek M., Otyepka M., Košinová P., Damborský J. CAVER: A program for molecular speleology. Proceedings from XX. Biochemický zjazd. 2006.
Otyepka M., Banáš P., Damborský J., Magistrato A., Carloni P. THE IMPORTANCE OF THE OXYANION HOLE IN ESTER HYDROLYSIS OF ENZYMATIC DEHALOGENTION CATALYZED BY HALOALKANE DEHALOGENASE REVEALED BY QM/MM CALCULATIONS. Proceedings from XX. Biochemický zjazd. 2006.
KAPITOLA V KNIZE
Šponer J., Otyepka M., Banáš P., Réblová K., Walter N. Innovations in Biomolecular Modeling and Simulations (Vol. 2 Chap. 6): Molecular Dynamics Simulations of RNA Molecules. Innovations in Biomolecular Modeling and Simulations Volume 2. 2012.
ABSTRAKT
Banáš P., Walter N., Šponer J., Otyepka M. Structural Insight into RNA Catalysis Revealed by Molecular Dynamics Simulations and QM/MM Calculation. Journal of Biomolecular Structure & Dynamics. 2009.
Filipová R., Banáš P., Otyepka M., Nevěčná T., Kvítek L. Stát se vědcem? Nové metody propagace přírodních věd mezi mládeží aneb Věda je zábava (2007). 2007.
Otyepka M., Banáš P., Damborský J., Magistrato A., Carloni P. Ester hydrolysis, the second reaction step of hydrolytic dehalogenation catalyzed by enzyme haloalkande dehalogenase from Sphingomonas paucimobilis UT26 in QM/MM focus. XIIth International Congress of Quantum Chemistry. 2006.
PŘEDNÁŠKA NEBO POSTER
Banáš P., Otyepka M., Rulíšek L., Svozil D., Šponer J. General base catalysis of hepatitis delta virus ribozyme self-cleavage reaction. FASEB Summer Research Conferences: Nucleic Acid Enzymes. .
Banáš P., Rulíšek L., Svozil D., Walter N., Šponer J., Otyepka M. Self-Cleavage Catalysis of the Hepatitis Delta Virus Ribozyme Investigated by QM/MM Calculations. The World Association of Theoretical and Computational Chemists - WATOC 2008. .
Florová P., Banáš P., Sklenovský P., Otyepka M. The Influence of Explicit Water Models on Proteins Structure and Stability Studied by Molecular Dynamic. ISOLATED BIOMOLECULES AND BIOMOLECULAR INTERACTIONS 2008. .
Banáš P., Otyepka M., Rulíšek L., Svozil D., Šponer J. General-base catalysis of hepatitis delta virus ribozyme self-cleavage reaction. Modeling Interaction in Biomolecules III. 2007.
SOFTWARE
Banáš P. H-bonds v1.0. 2009.
Banáš P. ResDist v1.0. 2009.
Banáš P. TheoChem library 1.0. 2009.

Uživatel nepovolil zobrazení dat v Portále UP.

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