Publications
_{Structural Bioinformatics}

Kanhema, T.; Parobczak, K.; Patil, S.; Holm-Kaczmarek, D.; Hallin, E.; Ludwiczak, J.; Szczepankiewicz, A.; Pauzin, F.; Mahboob, A.; Szum, A. et al.; Ishizuka, Y.; Dunin-Horkawicz, S.; Kursula, P.; Wilczynski, G.; Magalska, A.; Bramham, C.: Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles. Cell Reports 44 (4), 115525 (2025)

Madaj, R.; Martinez-Goikoetxea, M.; Kaminski, K.; Ludwiczak, J.; Dunin-Horkawicz, S.: Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains. Protein Science 34 (1), e5244 (2025)

Tomecki, R.; Drazkowska, K.; Madaj, R.; Mamot, A.; Dunin-Horkawicz, S.; Sikorski, P.: Expanding the available RNA labeling toolbox with CutA nucleotidyltransferase for efficient transcript labeling with purine and pyrimidine nucleotide analogs. ChemBioChem 25 (15), e202400202 (2024)

Winski, A.; Ludwiczak, J.; Orlowska, M.; Madaj, R.; Kaminski, K.; Dunin-Horkawicz, S.: AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Science 33 (1), e4846 (2024)

Smug, B.; Szczepaniak, K.; Riocha, E.; Dunin-Horkawicz, S.; Mostowy, R.: Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nature Communications 14 (1), 7460 (2023)

Kaminski, K.; Ludwiczak, J.; Pawlicki, K.; Alva, V.; Dunin-Horkawicz, S.: pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. Bioinformatics 39 (10), btad579 (2023)

Dunin-Horkawicz, S.: Coiled-coil domains hiding in the AlphaFold database. In 9th Alpbach Workshop on: Repeat Proteins – Biology & Design. 9th Alpbach Workshop: Repeat Proteins – Biology & Design, Alpbach, Austria, September 07, 2025 - September 11, 2025. (2025)

Dunin-Horkawicz, S.: What can we learn from incorrect AlphaFold2 models? (the case of signal transduction). In 76. Mosbacher Kolloquium "AI-driven (r)evolution in structural biology & protein design". 76. Mosbacher Kolloquium "AI-driven (r)evolution in structural biology & protein design", Mosbach, Germany, March 20, 2025 - March 23, 2025. (2025)

Smug, B.; Szczepaniak, K.; Dunin-Horkawicz, S.; Rocha, E.; Mostowy, R.: How phages play with LEGO: studying protein-level mosaicism in phages and its evolutionary implications. In The Local Pangenome, 40, p. 88. The Local Pangenome, Alicante, Spain, October 25, 2023 - October 28, 2023. (2023)

Madaj, R.; Orlowska, M.; Kaminski, K.; Pawlicki, K.; Dunin-Horkawicz, S.: Side mutants of connexin proteins as a cause of non-functional gap junction beta channels: a structural bioinformatics approach. In BioInformatics in Torun 2023 - BIT23, p. 16. BioInformatics in Torun 2023 (BIT23), Torun, Poland, June 29, 2023. (2023)

Orlowska, M.; Madaj, R.; Kubica, J.; Kaminski, K.; Dunin-Horkawicz, S.: Bioinformatics approach for programmed cell death receptor from Nostoc punctiforme. In BioInformatics in Torun 2023 - BIT23, p. 34. BioInformatics in Torun 2023 (BIT23), Torun, Poland, June 29, 2023. (2023)

Kubica, J.; Madaj, R.; Orlowska, M.; Krarkowski, K.; Gront, D.; Dunin-Horkawicz, S.: Modeling of a putative programmed cell death receptor from Nostoc punctiforme. In 10th Prof. Krzysztof W. Szewczyk Intercollegiate Biotechnology Symposium: SYMBIOZA, O-17, p. 52. 10th Prof. Krzysztof W. Szewczyk Intercollegiate Biotechnology Symposium: SYMBIOZA, Warsaw, Poland, May 12, 2023 - May 14, 2023. (2023)

Coles, M.; Dunin-Horkawicz, S.; Hartmann, M.; Lupas, A.: Revisiting HAMP in the AlphaFold age. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 12. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Lupas, A.; Dunin-Horkawicz, S.; Martinez-Goikoetxea, M.; Hartmann, M.; Hernandez Alvarez, B.: The structural diversity of natural coiled coils. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 39. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Madaj, R.; Kamiński, K.; Wiński, A.; Ludwiczak, J.; Dunin-Horkawicz, S.: Coiled-coil domains and AlphaFold2: friends or foes? In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 21. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Ptacek, J.; Albrecht, R.; Dunin-Horkawicz, S.; Schultz, J.; Coles, M.; Hartmann, M.; Lupas, A.: Archaeal receptor Af1503: an ideal model for structural and functional studies of transmembrane signaling. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 54. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Krakowski, K.; Łabędzka-Dmoch, K.; Golik, P.; Dunin-Horkawicz, S.: Functional analysis of prokaryotic homologs of programmed cell death factors. In Meeting of the EMBO Young Investigator Network on Computational Methods in Ecology and Evolutionary Biology of Microbes, p. 15. Meeting of the EMBO Young Investigator Network on Computational Methods in Ecology and Evolutionary Biology of Microbes, Chęciny, Poland, July 07, 2022 - July 09, 2022. (2022)

Kubica, J.; Gront, D.; Dunin-Horkawicz, S.: Modeling of a putative programmed cell death receptor. In Meeting of the EMBO Young Investigator Network on Computational Methods in Ecology and Evolutionary Biology of Microbes, p. 26. Meeting of the EMBO Young Investigator Network on Computational Methods in Ecology and Evolutionary Biology of Microbes, Chęciny, Poland, July 07, 2022 - July 09, 2022. (2022)

Dunin-Horkawicz, S.: What can we learn from incorrect AlphaFold2 models? The case of signal transduction. BioConnect Seminar: Max Planck Institute for Biology, Tübingen, Germany (2024)

Krakowski, K.; Orlowska, M.; Kaminski, M.; Bartosik, D.; Dunin-Horkawicz, S.: pLAST: a tool for rapid comparison and classification of bacterial plasmid sequences. (submitted)