Publication Records

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

LAMOTHE, Lucie, Jennifer R B JENSEN, Hans IENASESCU, Ove J R GUSTAFSSON, Alban GAIGNARD, Dmitry REPCHEVSKY, Radka SVOBODOVÁ, Tomáš RAČEK, Adrián ROŠINEC, Matej ANTOL and Hervé MÉNAGER. An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. BioHackrXiv. 2023, p. 1-10. Available from: https://dx.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 and Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. Nature Portfolio, 2023, vol. 10, No 1, p. 1-13. ISSN 2052-4463. Available from: https://dx.doi.org/10.1038/s41597-023-02778-9.

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ, Tomáš RAČEK and Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, vol. 51, W1, p. "W11"-"W16", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad349.

CHARESHNEU, Aliaksei, Adam MIDLIK, Crina-Maria IONESCU, Alexander ROSE, Vladimír HORSKÝ, Alessio CANTARA, Radka SVOBODOVÁ, Karel BERKA and 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, vol. 51, W1, p. "W326"-"W330", 5 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad411.

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 and Petr SVOBODA. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. CAMBRIDGE: CELL PRESS, 2022, vol. 82, No 21, p. 4064-4079. ISSN 1097-2765. Available from: https://dx.doi.org/10.1016/j.molcel.2022.10.010.

ILGOVÁ, Jana, Jiří VOREL, Pavel ROUDNICKÝ, Lucie ŠKORPÍKOVÁ, Martin HORN and 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, vol. 12, No 1, p. 1-18. ISSN 2045-2322. Available from: https://dx.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 and Christine A. ORENGO. CATH: increased structural coverage of functional space. Nucleic Acids Research. Oxford: Oxford University Press, 2021, vol. 49, D1, p. "D266"-"D273", 8 pp. ISSN 0305-1048. Available from: https://dx.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 and 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, vol. 49, W1, p. "W431"-"W437", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab314.

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Jaroslav KOČA, Karel BERKA and 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, vol. 13, No 1, p. 45-55. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-021-00528-w.

MIDLIK, Adam, Veronika NAVRÁTILOVÁ, Tarakaramji MOTURU, Jaroslav KOČA, Radka SVOBODOVÁ and K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Nature Scientific Reports. London: NATURE RESEARCH, 2021, vol. 11, No 1, p. 12345-12356. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-91494-8.