Výpis publikací

RAČEK, Tomáš; Dušan VEĽKÝ; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Ivana HUTAŘOVÁ VAŘEKOVÁ; Anna ŠPAČKOVÁ; Václav BAZGIER; Karel BERKA a Radka SVOBODOVÁ. MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update). Bioinformatics. Oxford University Press, 2025, roč. 41, č. 9, s. "btaf486", 5 s. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btaf486.

SCHINDLER, Ondřej; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Gabriela BUČEKOVÁ; Dominik TICHÝ; Karel BERKA a Radka SVOBODOVÁ. PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. Nucleic Acids Research. Oxford: Oxford University Press, 2025, roč. 53, W1, s. "W457"-"W462", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaf401.

PROCHÁZKA, David; Terézia SLANINÁKOVÁ; Jaroslav OĽHA; Adrián ROŠINEC; Katarína GREŠOVÁ; Miriama JÁNOŠOVÁ; Jakub ČILLÍK; Jana PORUBSKÁ; Radka SVOBODOVÁ; Vlastislav DOHNAL a Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W182"-"W186", 5 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae397.

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ a Karel BERKA. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In Lisacek, Frédérique. Protein Bioinformatics. 1. vyd. New York: Humana Press, 2024, s. 219-233. Methods in Molecular Biology 2836. ISBN 978-1-0716-4006-7. Dostupné z: https://doi.org/10.1007/978-1-0716-4007-4_12.

HOŠKOVÁ, Kateřina; Šárka FAJTLOVÁ; Tereza KUČEROVÁ; Pavel PLEVKA; Michal MIKL; Milan EŠNER a Radka SVOBODOVÁ. Core Facility Day Life Sciences 2024. 2024.

ROY CHOWDHURY, Riju; Marina FELIPE GROSSO; Darshak Chandulal GADARA; Zdeněk SPÁČIL; Veronika VIDOVÁ; Iva SOVADINOVÁ a Pavel BABICA. Cyanotoxin cylindrospermopsin disrupts lipid homeostasis and metabolism in a 3D in vitro model of the human liver. Chemico-Biological Interactions. Clare: Elsevier Ireland Ltd., 2024, roč. 397, July 2024, s. 1-15. ISSN 0009-2797. Dostupné z: https://doi.org/10.1016/j.cbi.2024.111046.

VOLLMAR, Melanie; Santosh TIRUNAGARI; Deborah HARRUS; David ARMSTRONG; Romana GÁBOROVÁ; Deepti GUPTA; Marcelo Querino Lima AFONSO; Genevieve EVANS a Sameer VELANKAR. Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature. Scientific Data. BERLIN: NATURE PORTFOLIO, 2024, roč. 11, č. 1, s. 1-18. ISSN 2052-4463. Dostupné z: https://doi.org/10.1038/s41597-024-03841-9.

MARTINEK, Vlastimil; Jessica MARTIN; Cedric BELAIR; Matthew J PAYEA; Sulochan MALLA; Panagiotis ALEXIOU a Manolis MARAGKAKIS. Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. NAR Genomics and Bioinformatics. Oxford University Press, 2024, roč. 6, č. 3, s. 1-9. ISSN 2631-9268. Dostupné z: https://doi.org/10.1093/nargab/lqae116.

DAR, Showkat Ahmad; Sulochan MALLA; Vlastimil MARTINEK; Matthew John PAYEA; Christopher Tai-Yi LEE; Jessica MARTIN; Aditya Jignesh KHANDESHI; Jennifer L MARTINDALE; Cedric BELAIR a Manolis MARAGKAKIS. Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress. eLife. ELIFE SCIENCES PUBLICATIONS LTD, 2024, roč. 13, December, s. 1-22. ISSN 2050-084X. Dostupné z: https://doi.org/10.7554/eLife.96284.

ŠPAČKOVÁ, Anna; Ondřej VÁVRA; Tomáš RAČEK; Václav BAZGIER; David SEHNAL; Jiří DAMBORSKÝ; Radka SVOBODOVÁ; David BEDNÁŘ a Karel BERKA. ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Research. Oxford University Press, 2024, roč. 52, D1, s. "D413"-"D418", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad1012.

EBRAHIMI NAGHANI, Shekoufeh; Ján ŠMERINGAI; Barbora PLESKAČOVÁ; Tereza DOBISOVÁ; Klára PANZAROVÁ; Markéta PERNISOVÁ a Helene ROBERT BOISIVON. Integrative phenotyping analyses reveal the relevance of the phyB-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperature. BMC PLANT BIOLOGY. ENGLAND: BMC, 2024, roč. 24, č. 1, s. 721-744. ISSN 1471-2229. Dostupné z: https://doi.org/10.1186/s12870-024-05394-w.

ROŠINEC, Adrián. Introduction to the new generation EGI container execution platform. In EGI Webinar programme 2024. 2024. Dostupné z: https://doi.org/10.5281/zenodo.10566759.

SIKORA, Maciej; Eva KLIMENTOVÁ; Dawid UCHAL; Denisa ŠRÁMKOVÁ; Agata P PERLINSKA; Mai Lan NGUYEN; Marta KORPACZ; Roksana MALINOWSKA; Szymon NOWAKOWSKI; Pawel RUBACH; Petr ŠIMEČEK a Joanna I SULKOWSKA. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Science. HOBOKEN: WILEY, 2024, roč. 33, č. 7, s. 1-21. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.4998.

LYČKA, Martin; Michal BUBENÍK; Michal ZÁVODNÍK; Vratislav PESKA; Petr FAJKUS; Martin DEMKO; Jiří FAJKUS a Miloslava FOJTOVÁ. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Research. Oxford: Oxford University Press, 2024, roč. 52, D1, s. "D311"-"D321", 11 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad672.

LAMOTHE, Lucie; Jennifer R B JENSEN; Hans IENASESCU; Ove J R GUSTAFSSON; Alban GAIGNARD; Dmitry REPCHEVSKY; Radka SVOBODOVÁ; Tomáš RAČEK; Adrián ROŠINEC; Matej ANTOL a Hervé MÉNAGER. An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. BioHackrXiv. 2023, s. 1-10. Dostupné z: https://doi.org/10.37044/osf.io/79kje.

APPASAMY, Sri Devan; John BERRISFORD; Romana GÁBOROVÁ; Sreenath NAIR; Stephen ANYANGO; Sergei GRUDININ; Mandar DESHPANDE; David ARMSTRONG; Ivanna PIDRUCHNA; Joseph I. J. ELLAWAY; Grisell Díaz LEINES; Deepti GUPTA; Deborah HARRUS; Mihaly VARADI a Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. Nature Portfolio, 2023, roč. 10, č. 1, s. 1-13. ISSN 2052-4463. Dostupné z: https://doi.org/10.1038/s41597-023-02778-9.

SCHINDLER, Ondřej; Karel BERKA; Alessio CANTARA; Aleš KŘENEK; Dominik TICHÝ; Tomáš RAČEK a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, roč. 51, W1, s. "W11"-"W16", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad349.

CHARESHNEU, Aliaksei; Adam MIDLIK; Crina-Maria IONESCU; Alexander ROSE; Vladimír HORSKÝ; Alessio CANTARA; Radka SVOBODOVÁ; Karel BERKA a David SEHNAL. Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Research. Oxford University Press, 2023, roč. 51, W1, s. "W326"-"W330", 5 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad411.

GREŠOVÁ, Katarína; Tomáš RAČEK; Vlastimil MARTINEK; David ČECHÁK; Radka SVOBODOVÁ a Panagiotis ALEXIOU. RBP-Tar – a searchable database for experimental RBP binding sites. F1000Research. Taylor and Francis, 2023, roč. 12, č. 755, s. 1-14. ISSN 2046-1402. Dostupné z: https://doi.org/10.12688/f1000research.131014.2.

VARADI, Mihaly; Stephen ANYANGO; Sri Devan APPASAMY; David ARMSTRONG; Marcus BAGE; John BERRISFORD; Preeti CHOUDHARY; Damian BERTONI; Mandar DESHPANDE; Grisell Diaz LEINES; Joseph ELLAWAY; Genevieve EVANS; Romana GÁBOROVÁ; Deepti GUPTA; Aleksandras GUTMANAS; Deborah HARRUS; Gerard J KLEYWEGT; Weslley Morellato BUENO; Nurul NADZIRIN; Sreenath NAIR; Lukas PRAVDA; Marcelo Querino Lima AFONSO; David SEHNAL; Ahsan TANWEER; James TOLCHARD; Charlotte ABRAMS; Roisin DUNLOP a Sameer VELANKAR. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Science. Wiley, 2022, roč. 31, č. 10, s. 1-10. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.4439.

ZAPLETAL, David; Eliska TABORSKA; Josef PASULKA; Radek MALIK; Karel KUBÍČEK; Martina ZÁNOVÁ; Christian MUCH; Marek ŠEBESTA; Valeria BUCCHERI; Filip HORVAT; Irena JENICKOVA; Michaela PROCHAZKOVA; Jan PROCHAZKA; Matyáš PINKAS; Jiří NOVÁČEK; Diego F JOSEPH; Radislav SEDLACEK; Carrie BERNECKY; Donal CARROLL; Richard ŠTEFL a Petr SVOBODA. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. CAMBRIDGE: CELL PRESS, 2022, roč. 82, č. 21, s. 4064-4079, 30 s. ISSN 1097-2765. Dostupné z: https://doi.org/10.1016/j.molcel.2022.10.010.

ILGOVÁ, Jana; Jiří VOREL; Pavel ROUDNICKÝ; Lucie ŠKORPÍKOVÁ; Martin HORN a Martin KAŠNÝ. Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host's body temperature. SCIENTIFIC REPORTS. ENGLAND: NATURE PORTFOLIO, 2022, roč. 12, č. 1, s. 1-18. ISSN 2045-2322. Dostupné z: https://doi.org/10.1038/s41598-022-14419-z.

SILLITOE, Ian; Nicola BORDIN; Natalie DAWSON; Vaishali P. WAMAN; Paul ASHFORD; Harry M. SCHOLES; Camilla S.M. PANG; Laurel WOODRIDGE; Clemens RAUER; Neeladri SEN; Mahnaz ABBASIAN; Sean LE CORNU; Su Datt LAM; Karel BERKA; Ivana HUTAŘOVÁ VAŘEKOVÁ; Radka SVOBODOVÁ; Jon LEES a Christine A. ORENGO. CATH: increased structural coverage of functional space. Nucleic Acids Research. Oxford: Oxford University Press, 2021, roč. 49, D1, s. "D266"-"D273", 8 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaa1079.

SEHNAL, David; S. BITTRICH; M. DESHPANDE; Radka SVOBODOVÁ; K. BERKA; V. BAZGIER; S. VELANKAR; S.K. BURLEY; Jaroslav KOČA a A.S. ROSE. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic acids research. Oxford: Oxford University Press, 2021, roč. 49, W1, s. "W431"-"W437", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkab314.

SCHINDLER, Ondřej; Tomáš RAČEK; Aleksandra MARŠAVELSKI; Jaroslav KOČA; Karel BERKA a Radka SVOBODOVÁ. Optimized SQE atomic charges for peptides accessible via a web application. Journal of Cheminformatics. Chemistry Central Ltd. in association with BioMed Central, 2021, roč. 13, č. 1, s. 45-55. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-021-00528-w.

MIDLIK, Adam; Veronika NAVRÁTILOVÁ; Tarakaramji MOTURU; Jaroslav KOČA; Radka SVOBODOVÁ a K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Nature Scientific Reports. London: NATURE RESEARCH, 2021, roč. 11, č. 1, s. 12345-12356. ISSN 2045-2322. Dostupné z: https://doi.org/10.1038/s41598-021-91494-8.