2023

1.

Chasák, Jan; Oorts, Lauren; Dak, Milan; Šlachtová, Veronika; Bazgier, Vaclav; Berka, Karel; De Vooght, Linda; Smiejkowska, Natalia; Van Calster, Kevin; Van Moll, Laurence; Cappoen, Davie; Cos, Paul; Brulíková, Lucie: Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation.. In: Bioorg. Med. Chem., vol. 95, no. 117504, 2023. (DOI)

2.

Špačková, Anna; Vávra, Ondřej; Tomáš Raček, Bazgier; Sehnal, David; Damborský, Jiří; Svobodová, Radka; Bednář, David; Berka, Karel: ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.. In: Nucleic Acids Res., vol. ASAP, no. gkad1012, 2023. (DOI)

3.

Majka, Maciej; Eva Jakobson Janáková, Irena; Jarve, Kadri; Cápal, Petr; Korchanová, Zuzana; Lampar, Adam; Juračka, Jakub; Valarik, Miroslav: The chromatin determinants and Ph1 gene effect at wheat sites with contrasting recombination frequency.. In: J. Adv. Res., vol. 53, no. 75-85, 2023. (DOI)

4.

Kadam, Shashikant A.; Sandoval, Stefania; Bastl, Zdenek; Simkovičová, Karolína; Kvítek, Libor; Jašík, Juraj; Olszowka, Joanna Elzbieta; Valtera, Stanislav; Vaidulych, Mykhailo; Morávková, Jaroslava; Sazama, Petr; Kubička, David; Travert, Arnaud; van Bokhoven, Jeroen A.; Fortunelli, Alessandro; Kleibert, Armin; Kalbáč, Martin; Vajda, Štefan: Cyclohexane Oxidative Dehydrogenation on Graphene-Oxide-Supported Cobalt Ferrite Nanohybrids: Effect of Dynamic Nature of Active Sites on Reaction Selectivity.. In: ACS Catal., vol. 13, iss. 20, pp. 13484-13505, 2023. (DOI)

5.

Voňka, Petr; Rárová, Lucie; Bazgier, Václav; Tichý, Vlastimil; Kolarova, Tamara; Holčáková, Jitka; Berka, Karel; Kvasnica, Miroslav; Oklešťková, Jana; Kudová, Eva; Strnad, Miroslav; Hrstka, Roman: Small change-big consequence: The impact of C15-C16 double bond in a D-ring of estrone on estrogen receptor activity.. In: J. Steroid Biochem. Mol. Biol. , vol. 233, no. 106365, 2023. (DOI)

6.

Coulon, Remi; Papoušková, Barbora; Mohammadi, Elmira; Otyepka, Michal; Wunnava, Sreekar; Šponer, Jiří; Šponer, Judit E: Prebiotic Synthesis of 3',5'-Cyclic Adenosine and Guanosine Monophosphates through Carbodiimide-Assisted Cyclization.. In: CHEMBIOCHEM, vol. ASAP, 2023. (DOI)

7.

Lapčíková, Barbora; Valenta, Tomáš; Lapčík, Lubomír; Li, Peng: Curcuma particle size evolution by application of bead milling process and curcuminoids content determination.. In: Int. J. Food Sci. Technol., vol. ASAP, 2023. (DOI)

8.

Mallada, Benjamin; Ondráček, M; Lamanec, Maximilián; Gallardo, A; Jimenez-Martin, A; de la Torre, Bruno; Hobza, Pavel; Jelínek, Pavel: Visualization of π-hole in molecules by means of Kelvin probe force microscopy.. In: Nat. Commun., vol. 14, iss. 1, no. 4954, 2023. (DOI)

9.

Love, Olivia; Galindo-Murillo, Rodrigo; Zgarbová, Marie; Šponer, Jiří; Jurečka, Petr; Cheatham, I. I. I. Thomas E.: Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.. In: J. Chem. Theory Comput., vol. 19, iss. 13, pp. 4299-4307, 2023. (DOI)

10.

Chareshneu, Aliaksei; Midlík, Adam; Ionescu, Crina-Maria; Rose, Alexander; Horský, Vladimír; Cantara, Alessio; Svobodová, Radka; Berka, Karel; Sehnal, David: Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.. In: Nucleic Acids Res., vol. 51, iss. W1, pp. W326-W330, 2023. (DOI)

11.

Řepka, David; Kurillová, Antonia; Murtaja, Yousef; Lapčík, Lubomír: Application of Physical-Chemical Approaches for Encapsulation of Active Substances in Pharmaceutical and Food Industries.. In: Foods, vol. 12, iss. 11, 2023. (DOI)

12.

Schindler, Ondřej; Berka, Karel; Cantara, Alessio; Křenek, Aleš; Tichý, Dominik; Raček, Tomáš; Svobodová, Radka: αCharges: partial atomic charges for AlphaFold structures in high quality. . In: Nucleic Acids Res., vol. 51, iss. W1, pp. W11-W16, 2023. (DOI)

13.

Lapčík, Lubomír; Řepka, David; Lapčíková, Barbora; Sumczynski, Daniela; Gautam, Shweta; Li, Peng; Valenta, Tomáš: A Physicochemical Study of the Antioxidant Activity of Corn Silk Extracts.. In: Foods, vol. 12, iss. 11, no. 2159, 2023. (DOI)

14.

Civiš, Svatopluk; Lamanec, Maximilian; Špirko, Vladimir; Kubišta, Jiří; Spet'ko, Matej; Hobza, Pavel: Hydrogen Bonding with Hydridic Hydrogen-Experimental Low-Temperature IR and Computational Study: Is a Revised Definition of Hydrogen Bonding Appropriate?. In: J. Am. Chem. Soc., vol. 145, iss. 15, pp. 8550-8559, 2023. (DOI)

15.

Lawson, Roland; Čechová, Petra; Zarrouk, Elies; Javellaud, James; Bazgier, Václav; Otyepka, Michal; Trouillas, Patrick; Picard, Nicolas; Marquet, Pierre; Saint-Marcoux, Franck; El Balkhi, Souleiman: Metabolic interactions of benzodiazepines with oxycodone ex vivo and toxicity depending on usage patterns in an animal model. In: Br. J. Pharmacol., vol. 180, iss. 7, pp. 829-842, 2023. (DOI)

16.

Belhacova, Lenka; Supinkova, Tatana; Panáček, Aleš; Hochvaldová, Lucie; Prucek, Robert; Zouzelka, Radek; Rathouský, Jiří: The role of TiO2 photocatalyst in degradation of halogenated phenols: Experimental, DFT and antibacterial study.. In: Appl. Catal., A , vol. 656, no. 119134, 2023. (DOI)

17.

Opustilová, Kristýna; Lapčíková, Barbora; Lapčík, Lubomír; Gautam, Shweta; Valenta, Tomáš; Li, Peng: Physico-Chemical Study of Curcumin and Its Application in O/W/O Multiple Emulsion. In: Foods, vol. 12, iss. 7, no. 1394, 2023. (DOI)

18.

Balouch, Martin; Kateřina, Storchmannová.; Štěpánek, František; Berka, Karel: Computational Prodrug Design Methodology for Liposome Formulability Enhancement of Small-Molecule APIs. . In: Mol. Pharmaceutics, vol. ASAP, 2023. (DOI)

19.

Lapčík, Lubomír; Sepetcioğlu, Harun; Murtaja, Yousef; Lapčíková, Barbora; Vašina, Martin; Ovsík, Martin; Staněk, Michal; Gautam, Shweta: Study of mechanical properties of epoxy/graphene and epoxy/halloysite nanocomposites.. 2023. (DOI)

20.

Anwar, Rehan; Navrátil, Jan; Vijayaraghavan, Rajani K.; McNally, Patrick J.; Otyepka, Michal; Blonski, Piotr; Sofianos, M. Veronica: Upcycling natural Limestone waste for thermochemical energy storage by utilising tailored CaZrO3 nanoadditives.. In: Mater. Adv., vol. 4, iss. 8, pp. 1905-1915, 2023. (DOI)

21.

Gautam, Shweta; Lapčík, Lubomír; Lapčíková, Barbora; Gál, Robert: Emulsion-Based Coatings for Preservation of Meat and Related Products.. In: Foods , vol. 12, iss. 4, no. 832, 2023. (DOI)

22.

Loubalová, Ivana; Zahradníková, Eva; Masaryk, Lukáš; Němec, Ivan; Hochvaldová, Lucie; Panáček, Aleš; Kvítek, Libor; Večeřová, Renata; Swiatkowski, Marcin; Kopel, Pavel: Antibacterial study on nickel and copper dicarboxylate complexes.. In: Inorg. Chim. Acta, vol. 545, no. 121273, 2023. (DOI)

2022

23.

Lapčík, Lubomír; Vašina, Martin; Lapčíková, Barbora; Bureček, Adam; Hružík, Lumír: Effect of rapeseed oil on the rheological, mechanical and thermal properties of plastic lubricants. In: Mech. Time-Depend. Mater. , vol. 26, pp. 33–47, 2022. (DOI)

24.

Dak, Milan; Šlachtová, Veronika; Šebela, Marek; Bazgier, Václav; Berka, Karel; Smiejkowska, Natalia; Oorts, Lauren; Cappoen, Davie; Brulíková, Lucie: Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function.. In: Eur. J. Med. Chem., vol. ASAP, 2022. (DOI)

25.

Lapčík, Lubomír; Lapčíková, Barbora; Gautam, Shweta; Vašina, Martin; Valenta, Tomáš; Řepka, David; Čépe, Klára; Rudolf, Ondřej: Acoustic and mechanical testing of commercial cocoa powders. In: Int. J. Food Prop. , vol. 25, iss. 1, pp. 2184–2197, 2022. (DOI)

26.

Midlik, Adam; Vařeková, Ivana Hutařová; Hutař, Jan; Chareshneu, Aliaksei; Berka, Karel; Svobodová, Radka: OverProt: secondary structure consensus for protein families. In: Bioinformatics, vol. 38, iss. 14, pp. 3648-3650, 2022. (DOI)

27.

Simkovičová, Karolína; Qadir, Muhammad I.; Žilková, Naděžda; Olszówka, Joanna E.; Sialini, Pavel; Kvítek, Libor; Vajda, Štefan: Hydrogenation of CO2 on Nanostructured Cu/FeOx Catalysts: The Effect of Morphology and Cu Load on Selectivity. In: Catalysts , vol. 12, iss. 5, no. 516, 2022. (DOI)

28.

Murtaja, Yousef; Lapčík, Lubomír Jr.; Lapčíková, Barbora; Gautam, Shweta; Vašina, Martin; Spanhel, Lubomír; Vlček, Jakub: Intelligent high-tech coating of natural biopolymer layers.. In: Adv. Colloid Interface Sci., vol. ASAP, 2022. (DOI)

29.

Kostelanská, Klára; Prudilová, Bláhová Barbora; Holešová, Sylva; Vlček, Jakub; Vetchý, David; Gajdziok, Jan: Comparative Study of Powder Carriers Physical and Structural Properties.. 2022. (DOI)

30.

Annadurai, Narendran; Malina, Lukáš; Salmona, Mario; Diomede, Luisa; Bastone, Antonio; Cagnotto, Alfredo; Romeo, Margherita; Šrejber, Martin; Berka, Karel; Otyepka, Michal; Hajdúch, Marián; Das, Viswanath: Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds. In: The FEBS journal, vol. 289, iss. 7, pp. 1929-1949, 2022. (DOI)

31.

Hochvaldová, Lucie; Panáček, David; Válková, Lucie; Prucek, Robert; Kohlová, Věra; Večeřová, Renata; Kolář, Milan; Kvítek, Libor; Panáček, Aleš: Restoration of antibacterial activity of inactive antibiotics via combined treatment with a cyanographene/Ag nanohybrid. In: Sci. Rep., vol. 12, no. 5222 , 2022. (DOI)

32.

Hochvaldová, Lucie; Večeřová, Renata; Kolář, Milan; Prucek, Robert; Kvítek, Libor; Lapčík, Lubomír; Panáček, Aleš: Antibacterial nanomaterials: Upcoming hope to overcome antibiotic resistance crisis. In: Nanotechnol. Rev., vol. 11, iss. 1, pp. 1115–1142, 2022. (DOI)

33.

Lapčíková, Barbora; Lapčík, Lubomír; Salek, Richardos; Tomáš Lorencová Valenta, Eva Vašina: Physical characterization of the milk chocolate using whey powder. In: LWT Food Sci. Technol., vol. 154, pp. 112669, 2022. (DOI)

34.

Lapčík, Lubomír; Vašina, Martin; Lapčíková, Barbora; Murtaja, Yousef: Effect of Conditioning on PU Foam Matrix Materials Properties.. In: Materials, vol. 15, no. 1, pp. 195, 2022. (DOI)

35.

Varadi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, Mandar; Nadzirin, Nurul; Nair, Sreenath S.; Pravda, Lukas; Tanweer, Ahsan; Al-Lazikani, Bissan; Andreini, Claudia; Barton, Geoffrey J.; Bednář, David; Berka, Karel; Blundell, Tom; Brock, Kelly P; Carazo, Jose Maria; Damborský, Jiří; David, Alessia; Dey, Sucharita; Dunbrack, Roland; Recio, Juan Fernandez; Fraternali, Franca; Gibson, Toby; Helmer-Citterich, Manuela; Hoksza, David; Hopf, Thomas; Jakubec, David; Kannan, Natarajan; Krivak, Radoslav; Kumar, Manjeet; Levy, Emmanuel D; London, Nir; Macias, Jose Ramon; Srivatsan, Madhusudhan M.; Marks, Debora S; Martens, Lennart; McGowan, Stuart A; McGreig, Jake E; Modi, Vivek; Parra, R. Gonzalo; Pepe, Gerardo; Piovesan, Damiano; Prilusky, Jaime; Putignano, Valeria; Radusky, Leandro G.; Ramasamy, Pathmanaban; Rausch, Atilio O.; Reuter, Nathalie; Rodriguez, Luis A.; Rollins, Nathan J; Rosato, Antonio; Rubach, Paweł; Serrano, Luis; Singh, Gulzar; Škoda, Petr; Sorzano, Carlos Oscar S.; Šťourač, Jan; Sulkowska, Joanna I; Svobodová, Radka; Tichshenko, Natalia; Tosatto, Silvio C. E.; Vranken, Wim; Wass, Mark N; Xue, Dandan; Zaidman, Daniel; Thornton, Janet; Sternberg, Michael; Orengo, Christine; Velankar, Sameer: PDBe-KB: collaboratively defining the biological context of structural data. In: Nucleic acids research, vol. 50, iss. D1, pp. D534-D542, 2022. (DOI)

36.

Murtaja, Yousef; Lapčík, Lubomír; Sepetcioglu, Harun; Vlček, Jakub; Lapčíková, Barbora; Ovsík, Martin; Staněk, Michal: Enhancement of the mechanical properties of HDPE mineral nanocomposites by filler particles modulation of the matrix plastic/elastic behavior.. In: Nanotechnol. Rev., vol. 11, no. 1, pp. 312-320, 2022. (DOI)

2021

37.

Martens, Marvin; Stierum, Rob; Schymanski, Emma L; Evelo, Chris T; Aalizadeh, Reza; Aladjov, Hristo; Arturi, Kasia; Audouze, Karine; Babica, Pavel; Berka, Karel; Bessems, Jos; Blaha, Ludek; Bolton, Evan E; Cases, Montserrat; Damalas, Dimitrios Ε; Dave, Kirtan; Dilger, Marco; Exner, Thomas; Geerke, Daan P; Grafström, Roland; Gray, Alasdair; Hancock, John M; Hollert, Henner; Jeliazkova, Nina; Jennen, Danyel; Jourdan, Fabien; Kahlem, Pascal; Klanova, Jana; Kleinjans, Jos; Kondic, Todor; Kone, Boï; Lynch, Iseult; Maran, Uko; Cuesta, Sergio Martinez; Ménager, Hervé; Neumann, Steffen; Nymark, Penny; Oberacher, Herbert; Ramirez, Noelia; Remy, Sylvie; Rocca-Serra, Philippe; Salek, Reza M; Sallach, Brett; Sansone, Susanna-Assunta; Sanz, Ferran; Sarimveis, Haralambos; Sarntivijai, Sirarat; Schulze, Tobias; Slobodnik, Jaroslav; Spjuth, Ola; Tedds, Jonathan; Thomaidis, Nikolaos; Weber, Ralf JM; van Westen, Gerard JP; Wheelock, Craig E; Williams, Antony J; Witters, Hilda; Zdrazil, Barbara; Županič, Anže; Willighagen, Egon L: ELIXIR and Toxicology: a community in development. In: F1000Research, vol. 10, iss. 1129, pp. 1129, 2021. (DOI)

38.

Prucek, Robert; Panáček, Aleš; Gajdová, Žaneta; Večeřová, Renata; Kvítek, Libor; Gallo, Jiří; Kolář, Milna: Specific detection of Staphylococcus aureus infection and marker for Alzheimer disease by surface enhanced Raman spectroscopy using silver and gold nanoparticle-coated magnetic polystyrene beads.. In: Sci. Rep., vol. 11, iss. 1, no. 6240, 2021. (DOI)

39.

Lo, Rabindranath; Manna, Debashree; Lamanec, Maximilian; Wang, Weizhou; Bakandritsos, Aristides; Dračinský, Martin; Zbořil, Radek; Nachtigallová, Dana; Hobza, Pavel: Addition Reaction between Piperidine and C60 to Form 1,4-Disubstituted C60 Proceeds through van der Waals and Dative Bond Complexes: Theoretical and Experimental Study.. In: J. Am. Chem. Soc., vol. ASAP, 2021. (DOI)

40.

Vařeková, Ivana Hutařová; Hutař, Jan; Midlik, Adam; Horský, Vladimír; Hladká, Eva; Svobodová, Radka; Berka, Karel: 2DProts: Database of Family-Wide Protein Secondary Structure Diagrams. In: Bioinformatics, pp. btab505, 2021. (DOI)

41.

Mallada, Benjamin; Blonski, Piotr; Langer, Rostislav; Jelínek, Pavel; Otyepka, Michal; Torre, Bruno: On-Surface Synthesis of One-Dimensional Coordination Polymers with Tailored Magnetic Anisotropy.. In: ACS Appl. Mater. Interfaces, vol. 13, no. 27, pp. 32393–32401, 2021. (DOI)

42.

Schindler, Ondřej; Raček, Tomáš; Marsavelsi, Aleksandra; Koča, Jaroslav; Berka, Karel; Svobodová, Radka: Optimized SQE atomic charges for peptides accessible via a web application. In: J Cheminf, vol. 13, no. 12, pp. 45, 2021. (DOI)

43.

Janeček, Michal; Kührová, Petra; Mlýnský, Vojtěch; Otyepka, Michal; Šponer, Jiří; Banáš, Pavel: W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.. In: J. Chem. Theory Comput., vol. 17, no. 6, pp. 3495–3509, 2021. (DOI)

44.

Midlik, Adam; Navrátilová, Veronika; Moturu, Taraka Ramji; Koča, Jaroslav; Svobodová, Radka; Berka, Karel: Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator. In: Scientific Reports, vol. 11, no. 1, pp. 12345, 2021. (DOI)

45.

Panáček, David; Hochvaldová, Lucie; Bakandritsos, Aristides; Malina, Tomáš; Langer, Michal; Belza, Jan; Martincová, Jana; Večeřová, Renata; Lazar, Petr; Poláková, Kateřina; Kolařík, Jan; Válková, Lucie; Kolář, Milan; Otyepka, Michal; Panáček, Aleš; Zbořil, Radek: Silver Covalently Bound to Cyanographene Overcomes Bacterial Resistance to Silver Nanoparticles and Antibiotics.. In: Adv. Sci., vol. 8, no. 12, pp. 2003090, 2021. (DOI)

46.

Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodová, Radka; Berka, Karel; Bazgier, Václav; Velankar, Sameer; Burley, Stephen K; Koča, Jaroslav; Rose, Alexander S: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.. In: Nucleic Acids Res., vol. 49, no. W1, pp. W431-W437, 2021. (DOI)

47.

Kiss, Márton A.; Peřina, Miroslav; Bazgier, Václav; May, Nóra V; Baji, Ádám; Jorda, Radek; Frank, Éva: Synthesis of dihydrotestosterone derivatives modified in the A-ring with (hetero)arylidene, pyrazolo[1,5-a]pyrimidine and triazolo[1,5-a]pyrimidine moieties and their targeting of the androgen receptor in prostate cancer.. In: J. Steroid Biochem. Mol. Biol., vol. 211, pp. 105904, 2021. (DOI)

48.

Braniša, Jana; Jomová, Klaudia; Lapčík, Lubomír; Porubská, Mária: Testing of electron beam irradiated sheep wool for adsorption of Cr(III) and Co(II) of higher concentrations.. In: Polym. Test., vol. 99, pp. 107191, 2021. (DOI)

49.

Zaoralová, Dagmar; Mach, Radim; Lazar, Petr; Medved', Miroslav; Otyepka, Michal: Single Atom Catalysts: Anchoring of Transition Metals to Graphene Derivatives as an Efficient Approach for Designing Single‐Atom Catalysts.. In: Adv. Mater. Interfaces, vol. 8, no. 8, pp. 2170041, 2021. (DOI)

50.

Ženata, Ondřej; Panáček, Aleš; Kvítek, Libor; Vrzal, Radim: The impact of graphene oxide on androgen receptor signalling in prostate cancer cells.. In: CHEMOSPHERE, vol. 269, pp. 128759, 2021. (DOI)