doc. RNDr. Karel Berka, Ph.D.

Tel: 58 563 4769, E-mail: karel.berka@upol.cz, Room: 3.009 RNDr. Karel Berka, Ph.D. orcid Google scholar ResearchGate

Research interests

Education

Employment

International experience

Cooperation

Grants, projects, awards, memberships

Supervized students

Ph.D.

Former students

Publications

2017

  1. Carazo Fernández A, Hyrsova L, Dušek J, Chodounská H, Horvátová A, Berka K, Bazgier V, Gan-Schreier H, Chamulitrat W, Kudová E, Pávek P: Acetylated deoxycholic (DCA) and cholic (CA) acids are potent ligands of pregnane X (PXR) receptor. Toxicol. Lett., 265, 86–96, 2017. (DOI)
  2. Huličiak M, Bazgier V, Berka K, Kubala M: RH421 binds into the ATP-binding site on the Na+/K+-ATPase. Biochim. Biophys. Acta, Gen. Subj., 1859(10), 2113–2122, 2017. (DOI)
  3. Navrátilová V, Paloncýová M, Berka K, Mise S, Haga Y, Matsumura C, Sakaki T, Inui H, Otyepka M: Molecular Insights into the Role of a Distal F240A Mutation that Alters CYP1A1 Activity towards Persistent Organic Pollutants. Biochim. Biophys. Acta, Gen. Subj., 1861(11), 2852-2860, 2017. (DOI)
  4. Otyepková E, Lazar P, Luxa J, Berka K, Cepe K, Sofer Z, Pumera M, Otyepka M: Surface properties of MoS2 probed by inverse gas chromatography and their impact on electrocatalytic properties. Nanoscale, ASAP, 2017. (DOI)
  5. Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J: ChannelsDB: database of biomacromolecular tunnels and pores. Nucleis Acids Res, ASAP, 2017. (DOI)
  6. Řezníčková E, Tenora L, Pospíšilová P, Galeta J, Jorda R, Berka K, Majer P, Potáček M, Kryštof V: ALK5 kinase inhibitory activity and synthesis of 2,3,4-substituted 5,5-dimethyl-5,6-dihydro-4H-pyrrolo[1,2-b]pyrazoles. Eur. J. Med. Chem., 127, 632–642, 2017. (DOI)

2016

  1. Baltus CB, Jorda R, Marot C, Berka K, Bazgier V, Kryštof V, Prié G, Viaud-Massuard M: Synthesis, Biological Evaluation and Molecular Modeling of a Novel Series of 7-Azaindole Based Tri-Heterocyclic Compounds as Potent CDK2/Cyclin E Inhibitors. Eur. J. Med. Chem., 108(27), 701–719, 2016. (DOI)
  2. Bazgier V, Berka K, Otyepka M, Banáš P: Exponential repulsion improves structural predictability of molecular docking. J. Comput. Chem., 37(28), 2485–2494, 2016. (DOI)
  3. Čechová P, Berka K, Kubala M: Ion pathways in the Na+/K+-ATPase. J. Chem. Inf. Model., 56(12), 2434–2444, 2016. (DOI)
  4. Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P: In Silico Pharmacology: Drug Membrane Partitioning and Crossing. Pharmacol. Res., 111, 471–486, 2016. (DOI)
  5. Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li J, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S: Tools and data services registry: a community effort to document bioinformatics resources. Nucl. Acids Res., 44(D1), D38-D47, 2016. (DOI)
  6. Kvasnica M, Oklešťková J, Bazgier V, Rárová L, Kořínková P, Mikulík J, Buděšínský M, Béres T, Berka K, Lu Q, Russinova E, Strnad M: Design, synthesis and biological activities of new brassinosteroid analogues with phenyl group in the side chain. Org. Biomol. Chem. , 14(37), 8691-8701, 2016. (DOI)
  7. Navrátilová V, Paloncýová M, Berka K, Otyepka M: Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J. Phys. Chem. B, 120(43), 11205–11213, 2016. (DOI)
  8. Nisler J, Kopečný D, Končitíková R, Zatloukal M, Bazgier V, Berka K, Zalabák D, Briozzo P, Strnad M, Spíchal L: Novel thidiazuron-derived inhibitors of cytokinin oxidase/dehydrogenase. Plant. Mol. Biol., 92(1), 235–248, 2016. (DOI)
  9. Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M: Role of Enzyme Flexibility in Ligand Access and Egress to Active Site – Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4 J. Chem. Theory Comput., 12(4), 2101–2109, 2016. (DOI)
  10. Scott EE, Wolf CR, Otyepka M, Humphreys SC, Reed JR, Henderson CJ, McLaughlin LA, Paloncýová M, Navrátilová V, Berka K, Anzenbacher P, Dahal UP, Barnaba C, Brozik JA, Jones JP, Estrada DF, Laurence JS, Park JW, Backes WL: The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function. Drug. Metab. Dispos., 44(4), 576-590, 2016. (DOI)

2015

  1. Carazo Fernández A, Smutný T, Hyrsová L, Berka K, Pávek P: Chrysin, baicalein and galangin are indirect activators of the human constitutive androstane receptor (CAR). Toxicol. Lett,, 233(2), 68-77, 2015. (DOI)
  2. Fabre G, Bayach I, Berka K, Paloncýová M, Starok M, Rossi C, Duroux J, Otyepka M, Trouillas P: Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes. Chem. Commun., 51(36), 7713-7716, 2015. (DOI)
  3. Fabre G, Hänchen A, Calliste C, Berka K, Banala S, Otyepka M, Süssmuth RD, Trouillas P: Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane. Bioorgan. Med. Chem., 23(15), 4866-4870, 2015. (DOI)
  4. Navrátilová V, Paloncyová M, Kajšová M, Berka K, Otyepka M: Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J. Chem. Inf. Model., 55(3), 628–635, 2015. (DOI)
  5. Paloncýová M, Vávrová K, Sovová Ž, DeVane R, Otyepka M, Berka K: Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails. J. Phys. Chem. B., 119(30), 9811-9819, 2015. (DOI)
  6. Řezníčková E, Popa A, Gucký T, Zatloukal M, Havlíček L, Bazgier V, Berka K, Jorda R, Popa I, Nasereddin A, Jaffe CL, Kryštof V, Strnad M: 2,6,9-Trisubstituted purines as CRK3 kinase inhibitors with antileishmanial activity in vitro. Bioorg. Med. Chem. Lett., 25(11), 2298-2301, 2015. (DOI)
  7. Řezníčková E, Weitensteiner S, Havlíček L, Jorda R, Gucký T, Berka K, Bazgier V, Zahler S, Kryštof V, Strnad M: Characterization of a Pyrazolo[4,3- d ]pyrimidine Inhibitor of Cyclin-Dependent Kinases 2 and 5 and Aurora A With Pro-Apoptotic and Anti-Angiogenic Activity In Vitro. Chem. Biol. Drug. Des., 86(6), 1528–1540, 2015. (DOI)
  8. Sovová Ž, Berka K, Otyepka M, Jurečka P: Coarse-Grain Simulations of Skin Ceramide NS with Newly Derived Parameters Clarify Structure of Melted Phase. J. Phys. Chem. B., 119(10), 3988-3998, 2015. (DOI)

2014

  1. de Beer TAP, Berka K, Thornton JM, Laskowski RA: PDBsum additions. Nucleic Acids Res., 42(D1), 292-296, 2014. (DOI)
  2. Holá K, Bourlinos AB, Kozák O, Berka K, Siskova KM, Havrdova M, Tuček J, Šafářová K, Otyepka M, Giannelis EP, Zbořil R: Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO− induced red-shift emission. Carbon, 70, 279-286, 2014. (DOI)
  3. Kvasnica M, Oklešťková J, Bazgier V, Rárová L, Berka K, Strnad M: Biological activities of new monohydroxylated brassinosteroid analogues with a carboxylic group in the side chain. Steroids, 85, 58-64, 2014. (DOI)
  4. Mojzych M, Šubertová V, Bielawska A, Bielawski K, Bazgier V, Berka K, Gucký T, Fornal E, Kryštof V: Synthesis and kinase inhibitory activity of new sulfonamide derivatives of pyrazolo[4,3-e][1,2,4]triazines. Eur. J. Med. Chem., 78, 217-224, 2014. (DOI)
  5. Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M: Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region. J. Phys. Chem. B, 118(4), 1030-1039, 2014. (DOI)
  6. Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M: Rationalization of Reduced Penetration of Drugs through Ceramide Gel Phase Membrane. Langmuir, 30(46), 13942-13948, 2014. (DOI)
  7. Paloncýová M, Fabre G, DeVane RH, Trouillas P, Berka K, Otyepka M: Benchmarking of Force Fields for Molecule–Membrane Interactions. J. Chem. Theory Comput., 10(9), 4143-4151, 2014. (DOI)
  8. Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M: Anatomy of enzyme channels. BMC Bioinf., 15(1), 379, 2014. (DOI)

2013

  1. Berka K, Paloncýová M, Anzenbacher P, Otyepka M: Behavior of Human Cytochromes P450 on Lipid Membranes. J. Phys. Chem. B, 117(39), 11556-11564, 2013. (DOI)
  2. Gucký T, Jorda R, Zatloukal M, Bazgier V, Berka K, Řezníčková E, Béres T, Strnad M, Kryštof V: A Novel Series of Highly Potent 2,6,9-Trisubstituted Purine Cyclin-Dependent Kinase Inhibitors. J. Med. Chem., 56(15), 6234-6247, 2013. (DOI)
  3. Havlíková M, Huličiak M, Bazgier V, Berka K, Kubala M: Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase. Biochim. Biophys. Acta, Biomembr., 1828(2), 568-576, 2013. (DOI)
  4. Paloncýová M, Berka K, Otyepka M: Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers. J. Phys. Chem. B, 117(8), 2403-2410, 2013. (DOI)
  5. Podloucká P, Berka K, Fabre G, Paloncýová M, Duroux J, Otyepka M, Trouillas P: Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant. J. Phys. Chem. B, 117(17), 5043-5049, 2013. (DOI)
  6. Pozharitskaya O, Shikov A, Makarova M, Ivanova S, Kosman V, Makarov V, Bazgier V, Berka K, Otyepka M, Ulrichová J: Antiallergic Effects of Pigments Isolated from Green Sea Urchin (Strongylocentrotus droebachiensis) Shells. Planta Med., 79(18), 1698-1704, 2013. (DOI)
  7. Sehnal D, Svobodová 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. J. Cheminf., 5(1), 1-39, 2013. (DOI)

2012

  1. Berka K, Anzenbacherová E, Hendrychová T, Lange R, Mašek V, Anzenbacher P, Otyepka M: Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site. J. Inorg. Biochem., 110, 46-50, 2012. (DOI)
  2. Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vařekova R, Koča J, Otyepka M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res., 40(W1), W222-W227, 2012. (DOI)
  3. Hendrychová T, Berka K, Navrátilová V, Anzenbacher P, Otyepka M: Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations. Curr. Drug Metab., 13(2), 177-189, 2012. (DOI)
  4. Košinová 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. (DOI)
  5. 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. (DOI)
  6. Paloncýová M, Berka K, Otyepka M: Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J. Chem. Theory Comput., 8(4), 1200-1211, 2012. (DOI)
  7. Řezanka M, Řezanka P, Míka L, Perlíková P, Berka K: Korespondenční seminář inspirovaný chemickou tématikou (KSICHT). Chem. Listy, 106, 317-340, 2012. (DOI)

2011

  1. Berka K, Hendrychová 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. (DOI)
  2. Berka K, Otyepka M: Insenstivity to Close Contacts and Inability to Predict Protein Foldability. J. Biomol. Struct. Dyn., 28(4), 633-634, 2011. (DOI)
  3. Ončák M, Berka K, Slavíček P: Novel Covalent Bond in Proteins: Calculations on Model Systems Question the Bond Stability. ChemPhysChem, 12(17), 3449-3457, 2011. (DOI)

2010

  1. Berka K, Laskowski RA, Hobza P, Vondrášek J: Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. J. Chem. Theory Comput., 6(7), 2191-2203, 2010. (DOI)
  2. Kolář M, Berka K, Jurečka P, Hobza P: On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. ChemPhysChem, 11(11), 2399-2408, 2010. (DOI)

2009

  1. Berka K, Hobza P, Vondrášek J: Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. ChemPhysChem, 10(3), 543-548, 2009. (DOI)

2008

  1. Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P: Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples. Collect. Czech. Chem. Commun., 73(10), 1261-1270, 2008. (DOI)