Publications of S Dunin-Horkawicz

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)

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)

Kamiński, K.; Ludwiczak, J.; Jasiński, M.; Bukala, A.; Madaj, R.; Szczepaniak, K.; Dunin-Horkawicz, S.: Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Briefings in Bioinformatics 23 (1), bbab371 (2022)

Zayats, V.; Perlinska, A.; Jarmolinska, A.; Jastrzebski, B.; Dunin-Horkawicz, S.; Sulkowska, J.: Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PLoS Computational Biology 17 (10), e1009502 (2021)

Adamczyk, M.; Lewicka, E.; Szatkowska, R.; Nieznanska, H.; Ludwiczak, J.; Jasiński, M.; Dunin-Horkawicz, S.; Sitkiewicz, E.; Swiderska, B.; Goch, G. et al.; Jagura-Burdzy , G.: Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiology 21 (1), 32 (2021)

Szczepaniak, K.; Bukala, A.; Marinho da Silva Neto, A.; Ludwiczak, J.; Dunin-Horkawicz, S.: A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics 36 (22-23), pp. 5368 - 5376 (2020)

Merski, M.; Młynarczyk, K.; Ludwiczak, J.; Skrzeczkowski, J.; Dunin-Horkawicz, S.; Górna, M.: Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 21 (1), 179 (2020)

Banaś , A.; Szczepaniak , A.; Plichta, M.; Bocian-Ostrzycka, K.; Dunin-Horkawicz, S.; Ludwiczak, J.; Płaczkiewicz, J.; Jagusztyn-Krynicka, E.: C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning. PLoS One 15 (3), e0230366 (2020)

Ludwiczak, J.; Winski, A.; Szczepaniak , A.; Alva, V.; Dunin-Horkawicz, S.: DeepCoil: a fast and accurate prediction of coiled-coil domains in protein sequences. Bioinformatics 35 (16), pp. 2790 - 2795 (2019)

Ludwiczak, J.; Winski, A.; Marinho da Silva Neto, A.; Szczepaniak, K.; Alva, V.; Dunin-Horkawicz, S.: PiPred: a deep-learning method for prediction of π-helices in protein sequences. Scientific Reports 9, 6888 (2019)

Nowacka, M.; Boccaletto, P.; Jankowska, A.; Jarzynka, T.; Bujnicki, J.; Dunin-Horkawicz, S.: RRMdb: an evolutionary-oriented database of RNA recognition motif sequences. Database: The Journal of Biological Databases and Curation 2019, bay148 (2019)

Boccaletto, P.; Magnus, M.; Almeida, C.; Zyla, A.; Astha, A.; Pluta, R.; Baginski, B.; Jankowska, A.; Dunin-Horkawicz, S.; Wirecki, T. et al.; Boniecki, M.; Stefaniak, F.; Bujnicki, J.: RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. Nucleic Acids Research (London) 46 (D1), pp. D202 - D205 (2018)

Machnicka, M.; Dunin-Horkawicz, S.; de Crécy-Lagard, V.; Bujnicki, J.: tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. Methods 107, pp. 34 - 41 (2016)

Korycinski, M.; Albrecht, R.; Ursinus, A.; Hartmann, M.; Coles, M.; Martin, J.; Dunin-Horkawicz, S.; Lupas, A.: STAC: A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems. Journal of Molecular Biology 427 (20), pp. 3327 - 3339 (2015)

Machnicka, M.; Kaminska, K.; Dunin-Horkawicz, S.; Bujnicki, J.: Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinformatics 16, 336 (2015)

Ferris, H.; Zeth, K.; Hulko, M.; Dunin-Horkawicz, S.; Lupas, A.: Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor. Journal of Structural Biology 186 (3), pp. 349 - 356 (2014)

Hartmann, M.; Dunin-Horkawicz, S.; Hulko, M.; Martin, J.; Coles, M.; Lupas, A.: A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity. Journal of Structural Biology 186 (3), pp. 357 - 366 (2014)

Dunin-Horkawicz, S.; Kopec, K.; Lupas, A.: Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis. Journal of Molecular Biology 426 (7), pp. 1568 - 1582 (2014)