Search Results - "Otyepka, M."

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes? by Krepl, M, Havrila, M, Stadlbauer, P, Banas, P, Otyepka, M, Pasulka, J, Stefl, R, Sponer, J

“…We report over 30 μs of unrestrained molecular dynamics simulations of six protein–RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0χOL3 RNA…”
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Quaternized carbon dot-modified graphene oxide for selective cell labelling--controlled nucleus and cytoplasm imaging by Datta, K K R, Kozák, O, Ranc, V, Havrdová, M, Bourlinos, A B, Safářová, K, Holá, K, Tománková, K, Zoppellaro, G, Otyepka, M, Zbořil, R

“…Cationic quaternized carbon dots (QCDs) and anionic graphene oxide sheets (GO) are combined via non-covalent interactions following a self-assembly pathway to…”
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beta-caryophyllene oxide and trans-nerolidol affect enzyme activity of CYP3A4 - in vitro and in silico studies by Špičáková, A, Bazgier, V, Skálová, L, Otyepka, M, Anzenbacher, P

“…Evaluation of possible interactions with enzymes of drug metabolism is an important part of studies on safety and, in general, on the properties of any drug or…”
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Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms by Chantemargue, B., Di Meo, F., Berka, K., Picard, N., Arnion, H., Essig, M., Marquet, P., Otyepka, M., Trouillas, P.

“…[Display omitted] The ABCC4/MRP4 exporter has a clinical impact on membrane transport of a broad range of xenobiotics. It is expressed at key locations for…”
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The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function by Scott, Emily E, Wolf, C Roland, Otyepka, Michal, Humphreys, Sara C, Reed, James R, Henderson, Colin J, McLaughlin, Lesley A, Paloncýová, Markéta, Navrátilová, Veronika, Berka, Karel, Anzenbacher, Pavel, Dahal, Upendra P, Barnaba, Carlo, Brozik, James A, Jones, Jeffrey P, Estrada, D Fernando, Laurence, Jennifer S, Park, Ji Won, Backes, Wayne L

“…This symposium summary, sponsored by the ASPET, was held at Experimental Biology 2015 on March 29, 2015, in Boston, Massachusetts. The symposium focused on: 1)…”
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Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains by Otyepka, M.

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On the rapid in situ oxidation of two-dimensional V2CTz MXene in culture cell media and their cytotoxicity by Jastrzębska, A.M., Scheibe, B., Szuplewska, A., Rozmysłowska-Wojciechowska, A., Chudy, M., Aparicio, C., Scheibe, M., Janica, I., Ciesielski, A., Otyepka, M., Barsoum, M.W.

“…The plethora of emerging two-dimensional (2D) materials exhibit wide potential application in novel technologies and advanced devices. However, their stability…”
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Covalent Graphene‐MOF Hybrids for High‐Performance Asymmetric Supercapacitors by Jayaramulu, Kolleboyina, Horn, Michael, Schneemann, Andreas, Saini, Haneesh, Bakandritsos, Aristides, Ranc, Vaclav, Petr, Martin, Stavila, Vitalie, Narayana, Chandrabhas, Scheibe, Błażej, Kment, Štěpán, Otyepka, Michal, Motta, Nunzio, Dubal, Deepak, Zbořil, Radek, Fischer, Roland A.

“…In this work, the covalent attachment of an amine functionalized metal‐organic framework (UiO‐66‐NH2 = Zr6O4(OH)4(bdc‐NH2)6; bdc‐NH2 =…”
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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr

“…We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the…”
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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters by Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr

“…We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as…”
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MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels by Berka, Karel, Hanák, Ondrej, Sehnal, David, Banás, Pavel, Navrátilová, Veronika, Jaiswal, Deepti, Ionescu, Crina-Maria, Svobodová Vareková, Radka, Koca, Jaroslav, Otyepka, Michal

“…Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based…”
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Computer Folding of RNA Tetraloops? Are We There Yet? by Kührová, Petra, Banáš, Pavel, Best, Robert B, Šponer, Jiří, Otyepka, Michal

“…RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5′-UNCG-3′ and…”
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In silico structural and functional analysis of fragments of the ankyrin repeat protein p18(INK4c) by Sklenovsý, P, Otyepka, M

“…Ankyrin repeat proteins (ARPs) are ubiquitous proteins that play critical regulatory roles in organisms and consist of repeating motifs (ankyrin repeats)…”
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Olomoucine II, New Effective CDK Inhibitor with Strong Cytotoxic Properties by Lenobel, R, Havli, L, Kryscaron, P V, Otyepka, M, Strnad, M

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Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics by Banáš, Pavel, Mládek, Arnošt, Otyepka, Michal, Zgarbová, Marie, Jurečka, Petr, Svozil, Daniel, Lankaš, Filip, Šponer, Jiří

“…Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA…”
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In vitro and in silico studies of interaction of synthetic 2,6,9-trisubstituted purine kinase inhibitors BPA-302, BP-21 and BP-117 with liver drug-metabolizing cytochromes P450 by Špičáková, A, Kraus, P, Gucký, T, Kryštof, V, Strnad, M, Bazgier, V, Otyepka, M, Kubíčková, V, Poruba, M, Rácová, Z, Zapletalová, I, Anzenbacher, P

“…An evaluation of possible interactions with enzymes of drug metabolism (cytochromes P450, CYP) is an important part of studies on safety and, in general, on…”
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Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs by Sklenovský, Petr, Florová, Petra, Banáš, Pavel, Réblová, Kamila, Lankaš, Filip, Otyepka, Michal, Šponer, Jiří

“…Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that…”
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Activation and inhibition of cyclin‐dependent kinase‐2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine‐rich loop by Bártová, Iveta, Otyepka, Michal, Kříž, Zdeněk, Koča, Jaroslav

“…Nanoseconds long molecular dynamics (MD) trajectories of differently active complexes of human cyclin‐dependent kinase 2 (inactive CDK2/ATP, semiactive…”
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Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/p25 and CDK2/Cyclin A Dynamics by Otyepka, Michal, Bártová, Iveta, Kříž, Zdeněk, Koča, Jaroslav

“…A detailed analysis is presented of the dynamics of human CDK5 in complexes with the protein activator p25 and the purine-like inhibitor roscovitine. These and…”
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Reference Simulations of Noncanonical Nucleic Acids with Different x Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA by Krepl, M, Zgarbova, M, Stadlbauer, P, Otyepka, M, Banas, P, Koca, J, Cheatham, TE III, Jurecka, P, Sponer, J

“…Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systems as possible. However, finding…”
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