| Year |
Citation |
Score |
| 2021 |
Annadurai N, Malina L, Salmona M, Diomede L, Bastone A, Cagnotto A, Romeo M, Šrejber M, Berka K, Otyepka M, Hajdúch M, Das V. Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds. The Febs Journal. PMID 34743390 DOI: 10.1111/febs.16270 |
0.398 |
|
| 2019 |
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. International Journal of Pharmaceutics. 118711. PMID 31593804 DOI: 10.1016/J.Ijpharm.2019.118711 |
0.304 |
|
| 2019 |
Juračka J, Šrejber M, Melíková M, Bazgier V, Berka K. MolMeDB: Molecules on Membranes Database. Database : the Journal of Biological Databases and Curation. 2019. PMID 31250015 DOI: 10.1093/Database/Baz078 |
0.372 |
|
| 2018 |
Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vareková R, Koca J, Otyepka M. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Research. 46: W368-W373. PMID 29718451 DOI: 10.1093/Nar/Gky309 |
0.533 |
|
| 2018 |
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. Journal of Inorganic Biochemistry. 183: 117-136. PMID 29653695 DOI: 10.1016/J.Jinorgbio.2018.03.002 |
0.565 |
|
| 2018 |
Chantemargue B, Di Meo F, Berka K, Picard N, 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. Pharmacological Research. PMID 29530601 DOI: 10.1016/J.Phrs.2018.02.029 |
0.532 |
|
| 2018 |
Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J. ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Research. 46: D399-D405. PMID 29036719 DOI: 10.1093/Nar/Gkx868 |
0.529 |
|
| 2018 |
Sehnal D, Deshpande M, Rose A, Pravda L, Midlik A, Svobodová Vařeková R, Mir S, Berka K, Velankar S, Koca J. Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite Biophysical Journal. 114: 47a. DOI: 10.1016/J.Bpj.2017.11.308 |
0.302 |
|
| 2018 |
Svobodova Varekova R, Midlik A, Hutarova Varekova I, Hutar J, Navratilova V, Koca J, Berka K. Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families Biophysical Journal. 114: 46a-47a. DOI: 10.1016/J.Bpj.2017.11.307 |
0.3 |
|
| 2018 |
Pravda L, Sehnal D, Berka K, Navrátilová V, Toušěk D, Bazgier V, Svobodová Vařeková R, Otyepka M, Koča J. Channelsdb and Moleonline - Database and Tool for Analysis of Biomacromolecular Tunnels and Pores Biophysical Journal. 114: 342a-343a. DOI: 10.1016/J.Bpj.2017.11.1912 |
0.471 |
|
| 2017 |
Otyepková E, Lazar P, Luxa J, Berka K, Čépe 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. PMID 29188849 DOI: 10.1039/C7Nr07342A |
0.478 |
|
| 2017 |
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. Biochimica Et Biophysica Acta. General Subjects. 1861: 2852-2860. PMID 28780123 DOI: 10.1016/J.Bbagen.2017.08.002 |
0.497 |
|
| 2017 |
Huličiak M, Bazgier V, Berka K, Kubala M. RH421 binds into the ATP-binding site on the Na/K-ATPase. Biochimica Et Biophysica Acta. Biomembranes. 1859: 2113-2122. PMID 28774819 DOI: 10.1016/J.Bbamem.2017.07.016 |
0.311 |
|
| 2017 |
Sehnal D, Deshpande M, Svobodova Varekova R, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koca J. Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution Biophysical Journal. 112: 178a. DOI: 10.1016/J.Bpj.2016.11.984 |
0.336 |
|
| 2017 |
Berka K, Sehnal D, Bazgier V, Pravda L, Svobodova-Varekova R, Otyepka M, Koca J. Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels Biophysical Journal. 112: 292a-293a. DOI: 10.1016/J.Bpj.2016.11.1585 |
0.555 |
|
| 2016 |
Čechová P, Berka K, Kubala M. Ion Pathways in the Na/K-ATPase. Journal of Chemical Information and Modeling. 56: 2434-2444. PMID 27966362 DOI: 10.1021/Acs.Jcim.6B00353 |
0.339 |
|
| 2016 |
Navrátilová V, Paloncýová M, Berka K, Otyepka M. Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. The Journal of Physical Chemistry. B. 120: 11205-11213. PMID 27723344 DOI: 10.1021/Acs.Jpcb.6B10108 |
0.567 |
|
| 2016 |
Bazgier V, Berka K, Otyepka M, Banáš P. Exponential repulsion improves structural predictability of molecular docking. Journal of Computational Chemistry. 37: 2485-94. PMID 27620738 DOI: 10.1002/Jcc.24473 |
0.551 |
|
| 2016 |
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. Pharmacological Research. 111: 471-486. PMID 27378566 DOI: 10.1016/J.Phrs.2016.06.030 |
0.536 |
|
| 2016 |
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. Journal of Chemical Theory and Computation. 12: 2101-9. PMID 26967371 DOI: 10.1021/Acs.Jctc.6B00075 |
0.552 |
|
| 2016 |
Scott EE, Wolf CR, Otyepka M, Humphreys SC, Reed JR, Henderson CJ, McLaughlin LA, Paloncyova M, Navratilova V, Berka K, Anzenbacher P, Dahal UP, Barnaba C, Brozik JA, Jones JP, et al. The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function. Drug Metabolism and Disposition: the Biological Fate of Chemicals. PMID 26851242 DOI: 10.1124/Dmd.115.068569 |
0.562 |
|
| 2016 |
Berka K, Sehnal D, Pravda L, Vařeková RS, Otyepka M, Koča J. MOLE – remastering of tool for detection and analysis of functional "void spaces" within biomacromolecules F1000research. 5. DOI: 10.7490/F1000Research.1113118.1 |
0.446 |
|
| 2015 |
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. The Journal of Physical Chemistry. B. 119: 9811-9. PMID 26151643 DOI: 10.1021/Acs.Jpcb.5B05522 |
0.526 |
|
| 2015 |
Fabre G, Hänchen A, Calliste CA, Berka K, Banala S, Otyepka M, Süssmuth RD, Trouillas P. Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane. Bioorganic & Medicinal Chemistry. PMID 26068016 DOI: 10.1016/J.Bmc.2015.05.031 |
0.528 |
|
| 2015 |
Fabre G, Bayach I, Berka K, Paloncýová M, Starok M, Rossi C, Duroux JL, Otyepka M, Trouillas P. Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes. Chemical Communications (Cambridge, England). 51: 7713-6. PMID 25851839 DOI: 10.1039/C5Cc00636H |
0.494 |
|
| 2015 |
Sovová Ž, Berka K, Otyepka M, Jurečka P. Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase. The Journal of Physical Chemistry. B. 119: 3988-98. PMID 25679231 DOI: 10.1021/Jp5092366 |
0.529 |
|
| 2015 |
Navrátilová V, Paloncýová M, Kajšová M, Berka K, Otyepka M. Effect of cholesterol on the structure of membrane-attached cytochrome P450 3A4. Journal of Chemical Information and Modeling. 55: 628-35. PMID 25654496 DOI: 10.1021/Ci500645K |
0.536 |
|
| 2014 |
Paloncýová M, Fabre G, DeVane RH, Trouillas P, Berka K, Otyepka M. Benchmarking of Force Fields for Molecule-Membrane Interactions. Journal of Chemical Theory and Computation. 10: 4143-51. PMID 26588554 DOI: 10.1021/Ct500419B |
0.548 |
|
| 2014 |
Pravda L, Berka K, Svobodová Va?eková R, Sehnal D, Banáš P, Laskowski RA, Ko?a J, Otyepka M. Anatomy of enzyme channels. Bmc Bioinformatics. 15: 379. PMID 25403510 DOI: 10.1186/S12859-014-0379-X |
0.515 |
|
| 2014 |
Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M. Rationalization of reduced penetration of drugs through ceramide gel phase membrane. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 13942-8. PMID 25354090 DOI: 10.1021/La503289V |
0.578 |
|
| 2014 |
Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M. Amphiphilic drug-like molecules accumulate in a membrane below the head group region. The Journal of Physical Chemistry. B. 118: 1030-9. PMID 24417480 DOI: 10.1021/Jp4112052 |
0.589 |
|
| 2014 |
Berka K, Paloncýová M, Anzenbacher P, Otyepka M. Membrane-bound human cytochrome P450 family: commonalities and differences F1000research. 5. DOI: 10.7490/F1000Research.1095644.1 |
0.496 |
|
| 2014 |
Hola K, Bourlinos AB, Kozak O, Berka K, Siskova KM, Havrdova M, Tucek J, Safarova K, Otyepka M, Giannelis EP, Zboril R. Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO- induced red-shift emission Carbon. 70: 279-286. DOI: 10.1016/J.Carbon.2014.01.008 |
0.471 |
|
| 2013 |
Pozharitskaya ON, Shikov AN, Makarova MN, Ivanova SA, Kosman VM, Makarov VG, Bazgier V, Berka K, Otyepka M, Ulrichová J. Antiallergic effects of pigments isolated from green sea urchin (Strongylocentrotus droebachiensis) shells. Planta Medica. 79: 1698-704. PMID 24288292 DOI: 10.1055/S-0033-1351098 |
0.501 |
|
| 2013 |
Berka K, Paloncýová M, Anzenbacher P, Otyepka M. Behavior of human cytochromes P450 on lipid membranes. The Journal of Physical Chemistry. B. 117: 11556-64. PMID 23987570 DOI: 10.1021/Jp4059559 |
0.557 |
|
| 2013 |
Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu CM, Otyepka M, Koča J. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics. 5: 39. PMID 23953065 DOI: 10.1186/1758-2946-5-39 |
0.529 |
|
| 2013 |
Podloucká P, Berka K, Fabre G, Paloncýová M, Duroux JL, Otyepka M, Trouillas P. Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant. The Journal of Physical Chemistry. B. 117: 5043-9. PMID 23560800 DOI: 10.1021/Jp3127829 |
0.529 |
|
| 2013 |
Paloncýová M, Berka K, Otyepka M. Molecular insight into affinities of drugs and their metabolites to lipid bilayers. The Journal of Physical Chemistry. B. 117: 2403-10. PMID 23387302 DOI: 10.1021/Jp311802X |
0.548 |
|
| 2013 |
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 Biochimica Et Biophysica Acta - Biomembranes. 1828: 568-576. PMID 23142565 DOI: 10.1016/J.Bbamem.2012.10.029 |
0.314 |
|
| 2012 |
Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vařeková R, Koča J, Otyepka M. MOLEonline 2.0: Interactive web-based analysis of biomacromolecular channels Nucleic Acids Research. 40. PMID 22553366 DOI: 10.1093/Nar/Gks363 |
0.526 |
|
| 2012 |
Paloncýová M, Berka K, Otyepka M. Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. Journal of Chemical Theory and Computation. 8: 1200-1211. PMID 22545027 DOI: 10.1021/Ct2009208 |
0.558 |
|
| 2012 |
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. Journal of Inorganic Biochemistry. 110: 46-50. PMID 22459173 DOI: 10.1016/J.Jinorgbio.2012.02.010 |
0.53 |
|
| 2012 |
Hendrychova T, Berka K, Navratilova V, Anzenbacher P, Otyepka M. Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Current Drug Metabolism. 13: 177-89. PMID 22208532 DOI: 10.2174/138920012798918408 |
0.525 |
|
| 2012 |
Otyepka M, Berka K, Anzenbacher P. Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450? Current Drug Metabolism. 13: 130-42. PMID 22208528 DOI: 10.2174/138920012798918372 |
0.534 |
|
| 2012 |
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. The Journal of Physical Chemistry. B. 116: 1309-18. PMID 22201287 DOI: 10.1021/Jp208731G |
0.54 |
|
| 2011 |
Berka K, Hendrychová T, Anzenbacher P, Otyepka M. Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site. The Journal of Physical Chemistry. A. 115: 11248-55. PMID 21744854 DOI: 10.1021/Jp204488J |
0.572 |
|
| 2011 |
Berka K, Otyepka M. Insenstivity to close contacts and inability to predict protein foldability. Journal of Biomolecular Structure & Dynamics. 28: 633-4; discussion 66. PMID 21142241 DOI: 10.1080/073911011010524969 |
0.511 |
|
| 2010 |
Berka K, Laskowski RA, Hobza P, Vondrášek J. Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. Journal of Chemical Theory and Computation. 6: 2191-203. PMID 26615945 DOI: 10.1021/Ct100007Y |
0.773 |
|
| 2010 |
Kolár M, Berka K, Jurecka P, Hobza P. On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 2399-408. PMID 20629063 DOI: 10.1002/Cphc.201000109 |
0.709 |
|
| 2010 |
Berka K, Laskowski RA, Hobza P, Vondrášek J. Energy matrix of structurally important side-chain/ side-chain interactions in proteins Journal of Chemical Theory and Computation. 6: 2191-2203. DOI: 10.1021/ct100007y |
0.57 |
|
| 2009 |
Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J. Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures. Journal of Chemical Theory and Computation. 5: 982-92. PMID 26609607 DOI: 10.1021/Ct800508V |
0.768 |
|
| 2009 |
Berka K, Hobza P, Vondrásek J. Analysis of energy stabilization inside the hydrophobic core of rubredoxin. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 10: 543-8. PMID 19170065 DOI: 10.1002/Cphc.200800401 |
0.768 |
|
| 2008 |
Biedermannova L, E. Riley K, Berka K, Hobza P, Vondrasek J. Another role of proline: Stabilization interactions in proteins and protein complexes concerning proline and tryptophane Physical Chemistry Chemical Physics. 10: 6350-6359. PMID 18972023 DOI: 10.1039/B805087B |
0.773 |
|
| 2008 |
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 Collection of Czechoslovak Chemical Communications. 73: 1261-1270. DOI: 10.1135/Cccc20081261 |
0.583 |
|
| 2008 |
Řezáč J, Berka K, Horinek D, Hobza P, Vondrášek J. The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies Collection of Czechoslovak Chemical Communications. 73: 921-936. DOI: 10.1135/Cccc20080921 |
0.598 |
|
| 2005 |
Mazna P, Berka K, Jelinkova I, Balik A, Svoboda P, Obsilova V, Obsil T, Teisinger J. Ligand binding to the human MT2 melatonin receptor: the role of residues in transmembrane domains 3, 6, and 7. Biochemical and Biophysical Research Communications. 332: 726-34. PMID 15913560 DOI: 10.1016/J.Bbrc.2005.05.017 |
0.611 |
|
| 2004 |
Mazna P, Obsilova V, Jelinkova I, Balik A, Berka K, Sovova Z, Ettrich R, Svoboda P, Obsil T, Teisinger J. Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding. Journal of Neurochemistry. 91: 836-42. PMID 15525337 DOI: 10.1111/J.1471-4159.2004.02758.X |
0.607 |
|
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