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BIOLOGICAL DATA MANAGEMENT AND ANALYSIS CORE FACILITY

 

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Publications

Publications

2026

  • Svoboda, T., Mikuš, M., Bohuš, L., Raček, T., Bučeková, G., Tichý, D., Berka, K., Svobodová, R., Schindler, O. PROPTIMUS LIVE: local constrained α-carbon optimization of proteins. Nucleic Acids Research. 2026, 54(W1), W301-W305. doi: 10.1093/nar/gkag511 [co-author] [acknowledged]
  • Ďuráčiová, R., Capandová, M., Berka, K., Svobodová, R., Slanináková, T., Kováč, K., Antol, M., Hejtmánek, L. Foldify: Web Application for Protein Structure Prediction. Journal of Chemical Information and Modeling. 2026, 66(13), 7762-7771. doi: 10.1021/acs.jcim.6c01154 [co-author] [acknowledged]
  • Mendes, A. I. S., Ienasescu, H., Andersen, Ch. A. T., Calhoun, E., Chmura, P. J., Collier, K., Goga, I., Gustafsson, O. J. R., Kalaš, M., Kierkegaard, M., Nielsen, N. K., Jaaniso, E., Jensen, J. R. B., Ludl, A., Ménager, H., Palmblad, M., Magyar, Z., Raček, T., Rošinec, A., ..., Schwämmle, V. bio.tools: an expanded web service for research software in the life sciences. Nucleic Acids Research. 2026. doi: 10.1093/nar/gkag420 [co-author] [acknowledged]
  • Raček, T., Pilát, M., Schindler, O., Bučeková, G., Tichý, D., Berka, K., Svobodová, R. Atomic Charge Calculator III: a modern platform for calculating partial atomic charges. Nucleic Acids Research. 2026. doi: 10.1093/nar/gkag379 [co-author] [acknowledged]
  • Bučeková, G., Doshchenko, V., Svoboda, T., Porubská, J., Chareshneu, A., Raček, T., Horský, V., Svobodová, R., Schindler, O. Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach. Journal of Cheminformatics. 2026, 18(1), 1-15. doi: 10.1186/s13321-026-01154-0 [co-author] [acknowledged]
  • Slanináková, T., Rošinec, A., Čillík, J., Křenek, A., Grešová, K., Porubská, J., Maršálková, E., Oľha, J., Procházka, D., Hejtmánek, L., Dohnal, V., Berka, K., Svobodová, R., Antol, M. AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts. Nucleic Acids Research. 2026. doi: 10.1093/nar/gkag372 [co-author] [acknowledged]

2025

  • Schindler, O., Svoboda, T., Rošinec, A., Raček, T., Bučeková, G., et al. PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. Nucleic Acids Research [online]. 2025, 53(W1), W457-W462. ISSN 0305-1048, doi: 10.1093/nar/gkaf401 [co-author] [acknowledged] 
  • Raček, T., Veľký, D., Bučeková, G., Schindler, O., Hutařová Vařeková, I., et al. MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update). Bioinformatics [online]. 2025, 41(9). ISSN 1367-4803, doi: 10.1093/bioinformatics/btaf486 [co-author] [acknowledged]
  • Rošinec, A., Slanináková, T., Pavlík, T., Randiak, R., Svoboda, T., et al. Gromacs MetaDump: a tool for extracting GROMACS simulation metadata. Journal of Cheminformatics [online]. 2025, 17(1), 160. ISSN 1758-2946, doi: 10.1186/s13321-025-01082-5 [co-author] [acknowledged]
  • Nevosád, L., Klodová, B., Rudolf, J., Raček, T., Přerovská, T., et al. GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte. The Plant Journal [online]. 2025, 121(5). ISSN 0960-7412, doi: 10.1111/tpj.70037 [co-author] [acknowledged]
  • Midlik, A., Bittrich, S., Fleming, J. R., Nair, S., Velankar, S., et al. MolViewSpec: a Mol* extension for describing and sharing molecular visualizations. Nucleic Acids Research [online]. 2025, 53(W1), W408-W414. ISSN 0305-1048, doi: 10.1093/nar/gkaf370 [acknowledged]
  • Berankova, M., Leoni, S., Holoubek, J., Haviernik, J., Salat, J., et al. Three-dimensional mapping of tick-borne encephalitis virus distribution in the mouse brain using a newly engineered TurboGFP reporter virus. Emerging Microbes & Infections [online]. 2025, 14(1). ISSN 2222-1751, doi: 10.1080/22221751.2025.2542246 [acknowledged]
  • Engebrecht, J., Calidas, A., Li, Q., Ruiz, A., Padture, P., et al. Loss of meiotic double strand breaks triggers recruitment of recombination-independent pro-crossover factors in C. elegans spermatogenesis. PLOS Genetics [online]. 2025, 21(10), e1011763. ISSN 1553-7404, doi: 10.1371/journal.pgen.1011763 [acknowledged]
  • Kusová, A., Holá, M., Petrová, I. G., Rudolf, J., Zachová, D., et al. TRB proteins in moss reveal their evolutionarily conserved roles in plant development and telomere maintenance. The Plant Journal [online]. 2025, 124(3). ISSN 0960-7412, doi: 10.1111/tpj.70574 [acknowledged]
  • Špačková, A., Kadášová, N., Hutařová Vařeková, I., Berka, K. Pathogenicity patterns in cytochrome P450 family. Bioinformatics Advances [online]. 2025, 5(1). ISSN 2635-0041, doi: 10.1093/bioadv/vbaf231 [co-author] [acknowledged]

2024

  • Procházka, D., Slanináková, T., Olha, J., Rošinec, A., Grešová, K., et al. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic Acids Research [online]. 2024, 52(W1), W182-W186. ISSN 0305-1048, doi: 10.1093/nar/gkae397 [co-author] [acknowledged]
  • Špačková, A., Vávra, O., Raček, T., Bazgier, V., Sehnal, D., et al. ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Research [online]. 2024, 52(D1), D413-D418. ISSN 0305-1048, doi: 10.1093/nar/gkad1012 [co-author] [acknowledged]
  • Špačková, A., Bazgier, V., Raček, T., Sehnal, D., Svobodová, R., et al. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In: Lisacek, F. (ed.). Protein Bioinformatics. Methods in Molecular Biology. New York, NY: Springer US, 2024, 219-233. ISBN 978-1-0716-4006-7, doi: 10.1007/978-1-0716-4007-4_12 [co-author] [acknowledged]
  • Turner, J., Abbott, S., Fonseca, N., Carrijo, L., Duraisamy, A. K., et al. EMDB-the Electron Microscopy Data Bank. Nucleic Acids Research. 2024, doi: 10.1093/nar/gkad1019 [co-author]
  • Ebrahimi Naghani, S., Šmeringai, J., Pleskačová, B., Dobisová, T., Panzarová, K., et al. Integrative phenotyping analyses reveal the relevance of the phyB-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperature. BMC Plant Biology [online]. 2024, 24(1). ISSN 1471-2229, doi: 10.1186/s12870-024-05394-w [acknowledged]
  • Chowdhury, R. R., Grosso, M. F., Gadara, D. C., Spáčil, Z., Vidová, V., et al. Cyanotoxin cylindrospermopsin disrupts lipid homeostasis and metabolism in a 3D in vitro model of the human liver. Chemico-Biological Interactions [online]. 2024, 397. ISSN 0009-2797, doi: 10.1016/j.cbi.2024.111046 [acknowledged]
  • Vollmar, M., Tirunagari, S., Harrus, D., Armstrong, D., Gáborová, R., et al. Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature. Scientific Data [online]. 2024, 11(1). ISSN 2052-4463, doi: 10.1038/s41597-024-03841-9 [co-author] [acknowledged]
  • Gresova, K., Racek, T., Martinek, V., Cechak, D., Svobodova, R., et al. RBP-Tar – a searchable database for experimental RBP binding sites. F1000Research [online]. 2023, 12. ISSN 2046-1402, doi: 10.12688/f1000research.131014.3 [co-author] [acknowledged]

2023

  • Schindler, O., Berka, K., Cantara, A., Křenek, A., Tichý, D., et al. ΑCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research [online]. 2023, 51(W1), W11-W16. ISSN 0305-1048, doi: 10.1093/nar/gkad349 [co-author] [acknowledged]
  • Chareshneu, A., Midlik, A., Ionescu, C.-M., Rose, A., Horský, V., et al. Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Research [online]. 2023, 51(W1), W326-W330. ISSN 0305-1048, doi: 10.1093/nar/gkad411 [co-author] [acknowledged]
  • Appasamy, S. D., Berrisford, J., Gaborova, R., Nair, S., Anyango, S., Grudinin, S., ..., Velankar, S. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. 2023, 10(1), 853. doi: 10.1038/s41597-023-02778-9 [co-author] [acknowledged]
  • Lamothe, L., Jensen, J. R. B., Ienasescu, H., Gustafsson, O. J. R., Gaignard, A., Repchevsky, D., Svobodová, R., Raček, T., Antol, M., Palmblad, M., Kalaš, M., Ménager, H. An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems. ELIXIR. 2023. ffhal-04206284f. doi: 10.37044/osf.io/79kje [co-author]
  • Balouch, M., Storchmannová, K., Štěpánek, F., Berka, K. Computational prodrug design methodology for liposome formulability enhancement of small-molecule APIs. Molecular Pharmaceutics. 2023, 20(4), 2119-2127. doi: 10.1021/acs.molpharmaceut.2c01078 [acknowledged]
  • Vonka, P., Rarova, L., Bazgier, V., Tichy, V., Kolarova, T., Holcakova, J., ..., Hrstka, R. Small change–big consequence: The impact of C15-C16 double bond in a D-ring of estrone on estrogen receptor activity. The Journal of Steroid Biochemistry and Molecular Biology. 2023, 233, 106365. doi: 10.1016/j.jsbmb.2023.106365 [acknowledged]
  • Chasák, J., Oorts, L., Dak, M., Šlachtová, V., Bazgier, V., Berka, K., ..., Brulíková, L. Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation. Bioorganic & Medicinal Chemistry. 2023, 95, 117504. doi: 10.1016/j.bmc.2023.117504 [acknowledged]

2022

  • Midlik, A., Hutařová Vařeková, I., Hutař, J., Chareshneu, A., Berka, K., Svobodová, R., Cowen, L. OverProt: secondary structure consensus for protein families. Bioinformatics [online]. 2022, 38(14), 3648-3650. ISSN 1367-4803, doi: 10.1093/bioinformatics/btac384 [co-author] [acknowledged]
  • Varadi, M., Anyango, S., Armstrong, D., et al. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Research [online]. 2022, 50(D1), D534-D542. ISSN 0305-1048, doi: 10.1093/nar/gkab988 [co-author] [acknowledged]
  • Annadurai, N., Malina, L., Salmona, M., Diomede, L., Bastone, A., Cagnotto, A., ..., Das, V. Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds. The FEBS Journal. 2022, 289(7), 1929-1949. doi: 10.1111/febs.16270 [acknowledged]
  • Dak, M., Šlachtová, V., Šebela, M., Bazgier, V., Berka, K., Smiejkowska, N., ..., Brulikova, L. Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function. European Journal of Medicinal Chemistry. 2022, 244, 114831. doi: 10.1016/j.ejmech.2022.114831 [acknowledged]
  • Varadi, M., Anyango, S., Appasamy, S. D., et al. 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 [online]. 2022, 31(10). ISSN 0961-8368, doi: 10.1002/pro.4439 [co-author]

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