Publikace

@article{Chasák2023,

title = {Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation.},

author = {Chasák, Jan and Oorts, Lauren and Dak, Milan and Šlachtová, Veronika and Bazgier, Vaclav and Berka, Karel and De Vooght, Linda and Smiejkowska, Natalia and Van Calster, Kevin and Van Moll, Laurence and Cappoen, Davie and Cos, Paul and Brulíková, Lucie},

doi = {10.1016/j.bmc.2023.117504},

year  = {2023},

date = {2023-11-15},

journal = {Bioorg. Med. Chem.},

volume = {95},

number = {117504},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Špačková2023,

title = {ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.},

author = {Špačková, Anna and Vávra, Ondřej and Raček, Tomáš, Bazgier, Václav and Sehnal, David and Damborský, Jiří and Svobodová, Radka and Bednář, David and Berka, Karel },

doi = {10.1093/nar/gkad1012},

year  = {2023},

date = {2023-11-13},

journal = {Nucleic Acids Res.},

volume = {ASAP},

number = {gkad1012},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Majka2023,

title = {The chromatin determinants and Ph1 gene effect at wheat sites with contrasting recombination frequency.},

author = {Majka, Maciej and Janáková, Eva Jakobson, Irena and Jarve, Kadri and Cápal, Petr and Korchanová, Zuzana and Lampar, Adam and Juračka, Jakub and Valarik, Miroslav},

doi = {10.1016/j.jare.2023.01.002},

year  = {2023},

date = {2023-11-01},

journal = {J. Adv. Res.},

volume = {53},

number = {75-85},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kadam2023,

title = {Cyclohexane Oxidative Dehydrogenation on Graphene-Oxide-Supported Cobalt Ferrite Nanohybrids: Effect of Dynamic Nature of Active Sites on Reaction Selectivity.},

author = {Kadam, Shashikant A. and Sandoval, Stefania and Bastl, Zdenek and Simkovičová, Karolína and Kvítek, Libor and Jašík, Juraj and Olszowka, Joanna Elzbieta and Valtera, Stanislav and Vaidulych, Mykhailo and Morávková, Jaroslava and Sazama, Petr and Kubička, David and Travert, Arnaud and van Bokhoven, Jeroen A. and Fortunelli, Alessandro and Kleibert, Armin and Kalbáč, Martin and Vajda, Štefan},

doi = {10.1021/acscatal.3c02592},

year  = {2023},

date = {2023-10-23},

journal = {ACS Catal.},

volume = {13},

issue = {20},

pages = {13484-13505},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Voňka2023,

title = {Small change-big consequence: The impact of C15-C16 double bond in a D-ring of estrone on estrogen receptor activity.},

author = {Voňka, Petr and Rárová, Lucie and Bazgier, Václav and Tichý, Vlastimil and Kolarova, Tamara and Holčáková, Jitka and Berka, Karel and Kvasnica, Miroslav and Oklešťková, Jana and Kudová, Eva and Strnad, Miroslav and Hrstka, Roman},

doi = {10.1016/j.jsbmb.2023.106365},

year  = {2023},

date = {2023-10-01},

journal = {J. Steroid Biochem. Mol. Biol. },

volume = {233},

number = {106365},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Coulon2023,

title = {Prebiotic Synthesis of 3',5'-Cyclic Adenosine and Guanosine Monophosphates through Carbodiimide-Assisted Cyclization.},

author = {Coulon, Remi and Papoušková, Barbora and Mohammadi, Elmira and Otyepka, Michal and Wunnava, Sreekar and Šponer, Jiří and Šponer, Judit E},

doi = {10.1002/cbic.202300510},

year  = {2023},

date = {2023-10-01},

journal = {CHEMBIOCHEM},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Curcuma particle size evolution by application of bead milling process and curcuminoids content determination.},

author = {Lapčíková, Barbora and Valenta, Tomáš and Lapčík, Lubomír and Li, Peng},

doi = {10.1111/ijfs.16671},

year  = {2023},

date = {2023-09-11},

journal = {Int. J. Food Sci. Technol.},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mallada2023,

title = {Visualization of π-hole in molecules by means of Kelvin probe force microscopy.},

author = {Mallada, Benjamin and Ondráček, M and Lamanec, Maximilián and Gallardo, A and Jimenez-Martin, A and de la Torre, Bruno and Hobza, Pavel and Jelínek, Pavel},

doi = {10.1038/s41467-023-40593-3},

year  = {2023},

date = {2023-07-22},

journal = {Nat. Commun.},

volume = {14},

number = {4954},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Love2023,

title = {Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.},

author = {Love, Olivia and Galindo-Murillo, Rodrigo and Zgarbová, Marie and Šponer, Jiří and Jurečka, Petr and Cheatham, I. I. I. Thomas E.},

doi = {10.1021/acs.jctc.3c00233},

year  = {2023},

date = {2023-06-07},

journal = {J. Chem. Theory Comput.},

volume = {19},

issue = {13},

pages = {4299-4307},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chareshneu2023,

title = {Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.},

author = {Chareshneu, Aliaksei and Midlík, Adam and Ionescu, Crina-Maria and Rose, Alexander and Horský, Vladimír and Cantara, Alessio and Svobodová, Radka and Berka, Karel and Sehnal, David},

doi = {10.1093/nar/gkad411},

year  = {2023},

date = {2023-06-05},

journal = {Nucleic Acids Res.},

volume = {51},

issue = {W1},

pages = {W326-W330},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Řepka2023,

title = {Application of Physical-Chemical Approaches for Encapsulation of Active Substances in Pharmaceutical and Food Industries.},

author = {Řepka, David and Kurillová, Antonia and Murtaja, Yousef and Lapčík, Lubomír},

doi = {10.3390/foods12112189},

year  = {2023},

date = {2023-05-30},

journal = {Foods},

volume = {12},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schindler2023,

title = {αCharges: partial atomic charges for AlphaFold structures in high quality. },

author = {Schindler, Ondřej and Berka, Karel and Cantara, Alessio and Křenek, Aleš and Tichý, Dominik and Raček, Tomáš and Svobodová, Radka},

doi = {10.1093/nar/gkad349},

year  = {2023},

date = {2023-05-01},

journal = {Nucleic Acids Res.},

volume = {51},

issue = {W1},

pages = {W11-W16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lapčík2023b,

title = {A Physicochemical Study of the Antioxidant Activity of Corn Silk Extracts.},

author = {Lapčík, Lubomír and Řepka, David and Lapčíková, Barbora and Sumczynski, Daniela and Gautam, Shweta and Li, Peng and Valenta, Tomáš},

doi = {10.3390/foods12112159},

year  = {2023},

date = {2023-05-01},

journal = {Foods},

volume = {12},

number = {2159},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Civiš2023,

title = {Hydrogen Bonding with Hydridic Hydrogen-Experimental Low-Temperature IR and Computational Study: Is a Revised Definition of Hydrogen Bonding Appropriate?},

author = {Civiš, Svatopluk and Lamanec, Maximilian and Špirko, Vladimir and Kubišta, Jiří and Spet'ko, Matej and Hobza, Pavel},

doi = {10.1021/jacs.3c00802},

year  = {2023},

date = {2023-04-15},

journal = {J. Am. Chem. Soc.},

volume = {145},

issue = {15},

pages = {8550-8559},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lawson2022,

title = {Metabolic interactions of benzodiazepines with oxycodone ex vivo and toxicity depending on usage patterns in an animal model},

author = {Lawson, Roland and Čechová, Petra and Zarrouk, Elies and Javellaud, James and Bazgier, Václav and Otyepka, Michal and Trouillas, Patrick and Picard, Nicolas and Marquet, Pierre and Saint-Marcoux, Franck and El Balkhi, Souleiman},

doi = {10.1111/bph.15765},

year  = {2023},

date = {2023-04-01},

urldate = {2022-01-26},

journal = {Br. J. Pharmacol.},

volume = {180},

issue = {7},

pages = {829-842},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Belhacova2023,

title = {The role of TiO2 photocatalyst in degradation of halogenated phenols: Experimental, DFT and antibacterial study.},

author = {Belhacova, Lenka and Supinkova, Tatana and Panáček, Aleš and Hochvaldová, Lucie and Prucek, Robert and Zouzelka, Radek and Rathouský, Jiří},

url = {10.1016/j.apcata.2023.119134},

doi = {10.1016/j.apcata.2023.119134},

year  = {2023},

date = {2023-03-28},

urldate = {2023-03-28},

journal = {Appl. Catal., A	},

volume = {656},

number = {119134},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Opustilová2023,

title = {Physico-Chemical Study of Curcumin and Its Application in O/W/O Multiple Emulsion},

author = {Opustilová, Kristýna and Lapčíková, Barbora and Lapčík, Lubomír and Gautam, Shweta and Valenta, Tomáš and Li, Peng},

year  = {2023},

date = {2023-03-25},

journal = {Foods},

volume = {12},

number = {1394},

issue = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Balouch2023,

title = {Computational Prodrug Design Methodology for Liposome Formulability Enhancement of Small-Molecule APIs. },

author = {Balouch, Martin and Storchmannová. Kateřina and Štěpánek, František and Berka, Karel},

doi = {10.1021/acs.molpharmaceut.2c01078},

year  = {2023},

date = {2023-03-20},

journal = {Mol. Pharmaceutics},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Anwar2023,

title = {Upcycling natural Limestone waste for thermochemical energy storage by utilising tailored CaZrO3 nanoadditives.},

author = {Anwar, Rehan and Navrátil, Jan and Vijayaraghavan, Rajani K. and McNally, Patrick J. and Otyepka, Michal and Blonski, Piotr and Sofianos, M. Veronica},

doi = {10.1039/d2ma01083f},

year  = {2023},

date = {2023-03-01},

journal = {Mater. Adv.},

volume = {4},

issue = {8},

pages = {1905-1915},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gautam2023,

title = {Emulsion-Based Coatings for Preservation of Meat and Related Products.},

author = {Gautam, Shweta and Lapčík, Lubomír and Lapčíková, Barbora and Robert Gál},

url = {https://www.mdpi.com/2304-8158/12/4/832},

doi = {10.3390/foods12040832},

year  = {2023},

date = {2023-02-15},

journal = {Foods },

volume = {12},

number = {832},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Loubalová2023,

title = {Antibacterial study on nickel and copper dicarboxylate complexes.},

author = {Loubalová, Ivana and Zahradníková, Eva and Masaryk, Lukáš and Němec, Ivan and Hochvaldová, Lucie and Panáček, Aleš and Kvítek, Libor and Večeřová, Renata and Swiatkowski, Marcin and Kopel, Pavel},

year  = {2023},

date = {2023-01-24},

journal = {Inorg. Chim. Acta},

volume = {545},

number = {121273},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lapčík2022c,

title = {Effect of rapeseed oil on the rheological, mechanical and thermal properties of plastic lubricants},

author = {Lapčík, Lubomír and Vašina, Martin and Lapčíková, Barbora and Bureček, Adam and Hružík, Lumír},

doi = {10.1007/s11043-020-09474-w},

year  = {2022},

date = {2022-12-01},

journal = {Mech. Time-Depend. Mater.	},

volume = {26},

pages = {33–47},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dak2022,

title = {Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function.},

author = {Milan Dak and Veronika Šlachtová and Marek Šebela and Václav Bazgier and Karel Berka and Natalia Smiejkowska and Lauren Oorts and Davie Cappoen and Lucie Brulíková},

url = {https://www.sciencedirect.com/science/article/pii/S0223523422007334#!},

doi = {10.1016/j.ejmech.2022.114831},

year  = {2022},

date = {2022-10-05},

journal = {Eur. J. Med. Chem.},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lapčík2022b,

title = {Acoustic and mechanical testing of commercial cocoa powders},

author = {Lapčík, Lubomír and Lapčíková, Barbora and Gautam, Shweta and Vašina, Martin and Valenta, Tomáš and Řepka, David and Čépe, Klára and Rudolf, Ondřej},

doi = {10.1080/10942912.2022.2127760},

year  = {2022},

date = {2022-09-29},

urldate = {2022-09-29},

journal = {Int. J. Food Prop.	},

volume = {25},

issue = {1},

pages = { 2184–2197},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Midlik2022,

title = {OverProt: secondary structure consensus for protein families},

author = {Adam Midlik and Ivana Hutařová Vařeková and Jan Hutař and Aliaksei Chareshneu and Karel Berka and Radka Svobodová},

doi = {10.1093/bioinformatics/btac384},

year  = {2022},

date = {2022-07-15},

journal = {Bioinformatics},

volume = {38},

issue = {14},

pages = {3648-3650},

abstract = {Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity.

Availability and implementation

OverProt Server is freely available at https://overprot.ncbr.muni.cz},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Simkovičová2022,

title = {Hydrogenation of CO2 on Nanostructured Cu/FeOx Catalysts: The Effect of Morphology and Cu Load on Selectivity},

author = {Karolína Simkovičová and Muhammad I. Qadir and Naděžda Žilková and Joanna E. Olszówka and Pavel Sialini and Libor Kvítek and Štefan Vajda},

url = {https://www.mdpi.com/2073-4344/12/5/516/htm},

doi = {10.3390/catal12050516},

year  = {2022},

date = {2022-05-04},

journal = {Catalysts },

volume = {12},

number = {516},

issue = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Murtaja2022b,

title = {Intelligent high-tech coating of natural biopolymer layers.},

author = {Murtaja, Yousef and Lubomír Jr. Lapčík and Lapčíková, Barbora and Gautam, Shweta and Vašina, Martin and Spanhel, Lubomír and Vlček, Jakub},

doi = {10.1016/j.cis.2022.102681},

year  = {2022},

date = {2022-04-22},

journal = {Adv. Colloid Interface Sci.},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Annadurai2022,

title = {Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds},

author = {Narendran Annadurai and Lukáš Malina and Mario Salmona and Luisa Diomede and Antonio Bastone and Alfredo Cagnotto and Margherita Romeo and Martin Šrejber and Karel Berka and Michal Otyepka and Marián Hajdúch and Viswanath Das},

doi = {10.1111/febs.16270},

year  = {2022},

date = {2022-04-01},

journal = {The FEBS journal},

volume = {289},

issue = {7},

pages = {1929-1949},

abstract = {Emerging experimental evidence suggests tau pathology spreads between neuroanatomically connected brain regions in a prion‐like manner in Alzheimer's disease (AD). Tau seeding, the ability of prion‐like tau to recruit and misfold naïve tau to generate new seeds, is detected early in human AD brains before the development of major tau pathology. Many antitumour drugs have been reported to confer protection against neurodegeneration, supporting the repurposing of approved and experimental or investigational oncology drugs for AD therapy. In this study, we evaluated whether antitumour drugs that abrogate the generation of seed‐competent aggregates of tau Repeat 3 (R3) domain peptides can prevent tau seeding and toxicity in Tau‐RD P301S FRET Biosensor cells and Caenorhabditis elegans. We demonstrate that drugs that interact with the N-terminal VQIVYK or the C-terminal region housing the Cys322 prevent R3 dimerisation, abolishing the generation of prion-like R3 seeds. Preformed R3 seeds (fibrils) capped with, or R3 seeds formed in the presence of VQIVYK- or Cys322-targeting drugs have a reduced potency to cause aggregation of naïve tau in biosensor cells and protect worms from aggregate toxicity. These findings indicate that VQIVYK- or Cys322-targeting drugs may act as prophylactic agents against tau seeding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hochvaldová2022,

title = {Restoration of antibacterial activity of inactive antibiotics via combined treatment with a cyanographene/Ag nanohybrid},

author = {Lucie Hochvaldová and David Panáček and Lucie Válková and Robert Prucek and Věra Kohlová and Renata Večeřová and Milan Kolář and Libor Kvítek and Aleš Panáček},

doi = {10.1038/s41598-022-09294-7},

year  = {2022},

date = {2022-03-25},

journal = {Sci. Rep.},

volume = {12},

number = {5222 },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hochvaldová2022b,

title = {Antibacterial nanomaterials: Upcoming hope to overcome antibiotic resistance crisis},

author = {Lucie Hochvaldová and Renata Večeřová and Milan Kolář and Robert Prucek and Libor Kvítek and Lapčík, Lubomír and Aleš Panáček},

doi = {10.1515/ntrev-2022-0059},

year  = {2022},

date = {2022-03-08},

journal = {Nanotechnol. Rev.},

volume = {11},

issue = {1},

pages = {1115–1142},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Physical characterization of the milk chocolate using whey powder},

author = {Lapčíková, Barbora and Lapčík, Lubomír and Salek, Richardos and Valenta, Tomáš Lorencová, Eva Vašina, Martin},

doi = {10.1016/j.lwt.2021.112669},

year  = {2022},

date = {2022-01-15},

journal = {LWT Food Sci. Technol.},

volume = {154},

pages = {112669},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lapčík2022,

title = {Effect of Conditioning on PU Foam Matrix Materials Properties.},

author = {Lapčík, Lubomír and Vašina, Martin and Lapčíková, Barbora and Murtaja, Yousef},

doi = {10.3390/ma15010195},

year  = {2022},

date = {2022-01-08},

journal = {Materials},

volume = {15},

number = {1},

pages = {195},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Varadi2022,

title = {PDBe-KB: collaboratively defining the biological context of structural data},

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

doi = {10.1093/nar/gkab988},

year  = {2022},

date = {2022-01-07},

urldate = {2022-01-07},

journal = {Nucleic acids research},

volume = {50},

issue = {D1},

pages = {D534-D542},

abstract = {The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Murtaja2022,

title = {Enhancement of the mechanical properties of HDPE mineral nanocomposites by filler particles modulation of the matrix plastic/elastic behavior.},

author = {Murtaja, Yousef and Lapčík, Lubomír and Sepetcioglu, Harun and Vlček, Jakub and Lapčíková, Barbora and Ovsík, Martin and Staněk, Michal},

doi = {10.1515/ntrev-2022-0023},

year  = {2022},

date = {2022-01-05},

urldate = {2022-01-05},

journal = {Nanotechnol. Rev.},

volume = {11},

number = {1},

pages = {312-320},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Martens2021,

title = {ELIXIR and Toxicology: a community in development},

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

doi = {10.12688/f1000research.74502.1},

year  = {2021},

date = {2021-11-08},

urldate = {2021-11-08},

journal = {F1000Research},

volume = {10},

issue = {1129},

pages = {1129},

abstract = {Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Prucek2021,

title = {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.},

author = {Robert Prucek and Aleš Panáček and Žaneta Gajdová and Renata Večeřová and Libor Kvítek and Jiří Gallo and Milna Kolář},

doi = {10.1038/s41598-021-84793-7},

year  = {2021},

date = {2021-07-17},

urldate = {2021-07-17},

journal = {Sci. Rep.},

volume = {11},

number = {6240},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lo2021b,

title = {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.},

author = {Rabindranath Lo and Debashree Manna and Maximilian Lamanec and Weizhou Wang and Aristides Bakandritsos and Martin Dračinský and Radek Zbořil and Dana Nachtigallová and Pavel Hobza},

doi = {10.1021/jacs.1c01542},

year  = {2021},

date = {2021-07-16},

journal = {J. Am. Chem. Soc.},

volume = {ASAP},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vařeková2021,

title = {2DProts: Database of Family-Wide Protein Secondary Structure Diagrams},

author = {Ivana Hutařová Vařeková and Jan Hutař and Adam Midlik and Vladimír Horský and Eva Hladká and Radka Svobodová and Karel Berka},

doi = {10.1093/bioinformatics/btab505},

year  = {2021},

date = {2021-07-09},

journal = {Bioinformatics},

pages = {btab505},

abstract = {Summary 

Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. 

 

Availability and Implementation 

Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mallada2021,

title = {On-Surface Synthesis of One-Dimensional Coordination Polymers with Tailored Magnetic Anisotropy.},

author = {Benjamin Mallada and Piotr Blonski and Rostislav Langer and Pavel Jelínek and Michal Otyepka and Bruno Torre},

doi = {10.1021/acsami.1c04693},

year  = {2021},

date = {2021-07-06},

journal = {ACS Appl. Mater. Interfaces},

volume = {13},

number = {27},

pages = {32393–32401},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schindler2021,

title = {Optimized SQE atomic charges for peptides accessible via a web application},

author = {Ondřej Schindler and Tomáš Raček and Aleksandra Marsavelsi and Jaroslav Koča and Karel Berka and Radka Svobodová},

doi = {10.1186/s13321-021-00528-w},

year  = {2021},

date = {2021-06-30},

journal = {J Cheminf},

volume = {13},

number = {12},

pages = {45},

abstract = {Background: Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations-e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible. 

 

Results: In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. 

 

Conclusion: The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application (https://acc2.ncbr.muni.cz) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Murray2021,

title = {W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.},

author = {Michal Janeček and Petra Kührová and Vojtěch Mlýnský and Michal Otyepka and Jiří Šponer and Pavel Banáš},

doi = {10.1021/acs.jctc.0c00976},

year  = {2021},

date = {2021-06-17},

journal = {J. Chem. Theory Comput.},

volume = {17},

number = {6},

pages = {3495–3509},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Midlik2021,

title = {Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator},

author = {Adam Midlik and Veronika Navrátilová and Taraka Ramji Moturu and Jaroslav Koča and Radka Svobodová and Karel Berka},

doi = {10.1038/s41598-021-91494-8},

year  = {2021},

date = {2021-06-11},

journal = {Scientific Reports},

volume = {11},

number = {1},

pages = {12345},

abstract = {Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)—a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Panáček2021,

title = {Silver Covalently Bound to Cyanographene Overcomes Bacterial Resistance to Silver Nanoparticles and Antibiotics.},

author = {David Panáček and Lucie Hochvaldová and Aristides Bakandritsos and Tomáš Malina and Michal Langer and Jan Belza and Jana Martincová and Renata Večeřová and Petr Lazar and Kateřina Poláková and Jan Kolařík and Lucie Válková and Milan Kolář and Michal Otyepka and Aleš Panáček and Radek Zbořil},

doi = {10.1002/advs.202003090},

year  = {2021},

date = {2021-05-20},

journal = {Adv. Sci.},

volume = {8},

number = {12},

pages = {2003090},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sehnal2021,

title = {Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.},

author = {David Sehnal and Sebastian Bittrich and Mandar Deshpande and Radka Svobodová and Karel Berka and Václav Bazgier and Sameer Velankar and Stephen K Burley and Jaroslav Koča and Alexander S Rose},

doi = {10.1093/nar/gkab314},

year  = {2021},

date = {2021-05-06},

journal = {Nucleic Acids Res.},

volume = {49},

number = {W1},

pages = {W431-W437},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kiss2021,

title = {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.},

author = {Márton A. Kiss and Miroslav Peřina and Václav Bazgier and Nóra V May and Ádám Baji and Radek Jorda and Éva Frank},

doi = {10.1016/j.jsbmb.2021.105904},

year  = {2021},

date = {2021-04-29},

journal = {J. Steroid Biochem. Mol. Biol.},

volume = {211},

pages = {105904},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braniša2021,

title = {Testing of electron beam irradiated sheep wool for adsorption of Cr(III) and Co(II) of higher concentrations.},

author = {Jana Braniša and Klaudia Jomová and Lubomír Lapčík and Mária Porubská},

url = {https://www.sciencedirect.com/science/article/pii/S0142941821001410},

doi = {10.1016/j.polymertesting.2021.107191},

year  = {2021},

date = {2021-04-24},

journal = {Polym. Test.},

volume = {99},

pages = {107191},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zaoralová2021,

title = {Single Atom Catalysts: Anchoring of Transition Metals to Graphene Derivatives as an Efficient Approach for Designing Single‐Atom Catalysts.},

author = {Dagmar Zaoralová and Radim Mach and Petr Lazar and Miroslav Medved' and Michal Otyepka},

doi = {10.1002/admi.202170041},

year  = {2021},

date = {2021-04-23},

journal = {Adv. Mater. Interfaces},

volume = {8},

number = {8},

pages = {2170041},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ženata2021,

title = {The impact of graphene oxide on androgen receptor signalling in prostate cancer cells.},

author = {Ondřej Ženata and Aleš Panáček and Libor Kvítek and Radim Vrzal},

doi = {10.1016/j.chemosphere.2020.128759},

year  = {2021},

date = {2021-04-15},

journal = {CHEMOSPHERE},

volume = {269},

pages = {128759},

keywords = {},

pubstate = {published},

tppubtype = {article}

}