Tel: 58 563 4769, E-mail: karel.berka@upol.cz, Room: 3.009 RNDr. Karel Berka, Ph.D.
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Research interests

  • Interaction of small drug-like molecules with biological membranes (MolMeDB)
  • in silico drug design (molecular docking, chemoinformatics)
  • Drug metabolism (cytochromes P450)
  • Structural bioinformatics (ELIXIR-CZ)

Education

  • 2016: doc. (habilitation) Physical chemistry, Palacký University, Olomouc
  • 2006 – 2010: Ph.D. Modelling of chemical properties of nano- and biomaterials, Faculty of Science, Charles University in Prague with collaboration of Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic (prof. Hobza)
  • 2008: RNDr. Physical chemistry, Faculty of Science, Charles University in Prague
  • 2001 – 2006: M.Sc. Physical chemistry, Faculty of Science, Charles University in Prague (prof. Obšil)

Employment

  • 2010 – now: Assistant professor, Department of Physical Chemistry, Palacký University, Olomouc
  • 2010 – now: Junior researcher, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc
  • 2007 – 2010: Ph.D. student, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague
  • 2003 – 2006: Technician, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague
  • 2002 – 2003: Technician, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague

International experience

Cooperation

  • Miroslav Strnad, Vladimír Kryštof, Lukáš Spíchal – Faculty of Science, Palacký University, Olomouc, CZ – in silico drug design
  • Jaroslav Koča, Radka Svobodová-Vařeková, David Sehnal – CEITEC, Masaryk University, Brno, Czech Republic – bioinformatic tools (MOLE)
  • Patrick Trouillas, Gabin Fabre – University of Limoges, France – antioxidants on membranes
  • Jiří Vondrášek – Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic – bioinformatics (ELIXIR-CZ infrastructure)
  • Pavel Anzenbacher, Eva Anzenbacherová – Faculty of Medicine and Dentistry, Palacký University, Olomouc, CZ – cytochrome P450
  • Martin Kubala – Faculty of Science, Palacký University, Olomouc, CZ – Na/K-ATPase
  • Kateřina Vávrová – Faculty of Pharmacy, Charles University, Hradec Králové, Czech Republic – skin lipids
  • Christel Bergstrom, Per Larson, Par Mattson – Department of Pharmacy, Uppsala University, SWE – passive permetation and drug solubility
  • Russell DeVane, Bruce Murch, Joanna Jaworska – Modelling&Simulation Unit, P&G, Ohio, USA – skin penetration
  • and others

Grants, projects, awards, memberships

  • MŠMT Barrande/Mobility 7AMB17FR026 Atomistic description of ABCC4/MRP4 membrane transporter: towards clinical applications (with: Pharmacologie des Immunosuppresseurs et Transplantation, INSERM (850), Limoges, France) 2017-2018
  • GACR 17-21122S MolMeDB – Validated Predictions of Small Molecule Interactions with Biological Membranes (PI, 4,5 MCZK) 2017-2019
  • Associate Member of Royal Society of Chemistry (AMRSC), 2015-

  • MEYS LM2015047: ELIXIR-CZ Czech National Infrastructure for Biological Data (co-PI, 2 MCZK) 2016-17

  • GACR P303/12/P019: Mechanism of ligand access/egress to/from active site of microsomal drug-metabolising cytochromes P450 (PI, 1 MCZK), 2012-2014
  • RCPTM award, Palacky University, Olomouc, 2012
  • Dean award, Faculty of Science, Palacky University, Olomouc, 2010-2013
  • 2nd best Poster Award, Prostab, Exeter, UK, 2007

Supervized students

Ph.D.

  • Martin Šrejber (2016-) – Modelling of Biomembranes

Former students

  • Veronika Navrátilová (2014-2018) – Behaviour of Membrane-bound Cytochrome P450 Enzymes. (co-supervision with prof. Otyepka)
  • Václav Bazgier (2011-2018) – Molecular Docking of Plant Regulators into Plant Receptors. (co-supervision with prof. Strnad)
  • Markéta Paloncýová, Ph.D. (2012-2016) – Modeling of Interactions of Small Molecules with Biomembranes. (co-supervision with prof. Otyepka)

Publications

2021

  1. Balouch M, Šrejber M, Šoltys M, Janská P, Štěpánek F, Berka K: In-silico screening of drug candidates for thermoresponsive liposome formulations Mol. Syst. Des. Eng., 6, 368-380, 2021. (DOI)
  2. Hutařová Vařeková I, Hutař J, Midlik A, Horský V, Hladká E, Svobodová R, Berka K: 2DProts: Database of Family-Wide Protein Secondary Structure Diagrams Bioinformatics, btab505, 2021. (DOI)
  3. Midlik A, Navrátilová V, Moturu TR, Koča J, Svobodová R, Berka K: Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator Scientific Reports, 11(1), 12345, 2021. (DOI)
  4. Schindler O, Raček T, Marsavelsi A, Koča J, Berka K, Svobodová R: Optimized SQE atomic charges for peptides accessible via a web application J Cheminf, 13(12), 45, 2021. (DOI)
  5. Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, Velankar S, Burley SK, Koča J, Rose AS: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res., 49(W1), W431-W437, 2021. (DOI)
  6. Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, … , Berka K, Hutařová Vařeková I, Svobodová R, Lees J, Orengo CA: CATH: increased structural coverage of functional space Nucl Acids Res, 49, 266–273, 2021. (DOI)

2020

  1. Berka P, Berka K, Doležal P: Dextrans as Permeation Markers and Carriers for Oral Transmucosal Drug Delivery Chem Listy, 114(8), 552-558, 2020. (DOI)
  2. Kubiasová K, Montesinos JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L: Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum Nat Commun, 11, 4285, 2020. (DOI)
  3. Raček T, Schindler O, Toušek D, Horský V, Berka K, Koča J, Svobodová R: Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res., gkaa367, 2020. (DOI)
  4. Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J: High-performance macromolecular data delivery and visualization for the web Acta Cryst D, 76(12), D76, 2020. (DOI)
  5. Šlachtová V, Šebela M, Torfs E, oorts L, Cappoen D, Berka K, Bazgier V, Brulíková L: Novel thiazolidinedione-hydroxamates as inhibitors of Mycobacterium tuberculosis virulence factor Zmp1. Eur. J. Med. Chem., 185, 111812, 2020. (DOI)

2019

  1. Berka P, Stránská D, Semecký V, Berka K, Doležal P: In vitro testing of flash-frozen sublingual membranes for storage and reproducible permeability studies of macromolecular drugs from solution or nanofiber mats. Int. J. Pharm., 572, 118711, 2019. (DOI)
  2. Jorda R, Řezníčková E, Kiełczewska U, Maj J, Morzycki J, Siergiejczyk L, Bazgier V, Berka K, Rárová L, Wojtkielewicz A: Synthesis of novel galeterone derivatives and evaluation of their in vitro activity against prostate cancer cell lines. Eur. J. Med. Chem., 179, 483-492, 2019. (DOI)
  3. Juračka J, Šrejber M, Melíková M, Bazgier V, Berka K: MolMeDB: Molecules on Membranes Database. Database, 2019, baz078, 2019. (DOI)
  4. Varadi M, Berrisford J, Deshpande M, Nair SS, Gutmanas A, Berka K, … , Koča J, … , Velankar S: PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res., gkz853, 2019. (DOI)

2018

  1. Berka K, Sršeň Š, Slavíček P: Je strojové učení budoucností teoretické chemie? Chemické listy, 112(10), 640-647, 2018. (DOI)
  2. Chantemargue B, Di Meo F, Berka K, Nicolas P, Arnion H, Essig M, Marquet P, Otyepka M, Trouillas P: Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms. Pharmacol. Res., 133, 318-327, 2018. (DOI)
  3. Gucký T, Řezníčková E, Muchová RT, Jorda R, Klejová Z, Malíková V, Berka K, Bazgier V, Ajani H, Lepšík M, Divoký V, Kryštof V: Discovery of N2-(4-Amino-cyclohexyl)-9-cyclopentyl-N6-(4-morpholin-4-ylmethyl-phenyl)-9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 mutations. J. Med. Chem., 61(9), 3855–3869, 2018. (DOI)
  4. Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J: ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res, 46(D1), D399–D405, 2018. (DOI)
  5. Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res, 46(W1), W368–W373, 2018. (DOI)
  6. Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M: Membrane-attached mammalian cytochromes P450: An overview of the membrane’s effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem, 183, 117-136, 2018. (DOI)

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, Biomembranes, 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, 9, 19236-19244, 2017. (DOI)
  5. 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)
  6. Sehnal D, Deshpande M, Svobodová Vařeková R, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J: LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data Nature Methods, 14, 1121–1122, 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)