Publications of J Ludwiczak

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)

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)

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)

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)

Ludwiczak, J.; Winski, A.; Hernandez-Alvarez, B.; Alva, V.; Malicki, M.; Marinho da Silva Neto, A.; Szczepaniak, K.; Dunin-Horkawicz, S.: Machine learning and simulation methods for deciphering sequence-structure relationships in proteins. In BioInformatics in Torun 2019 - BIT19, p. 4. BioInformatics in Torun 2019 (BIT19), Torun, Poland, June 27, 2019 - June 29, 2019. (2019)

Ludwiczak, J.; Wiński, A.; Marinho da Silva Neto, A.; Szczepaniak, K.; Alva, V.; Dunin-Horkawicz, S.: PiPred: a deep-learning method for prediction of pi-helices in protein sequences. In BioInformatics in Torun 2019 - BIT19, p. 61. BioInformatics in Torun 2019 (BIT19), Torun, Poland, June 27, 2019 - June 29, 2019. (2019)

Ludwiczak, J.; Wiński, A.; Szczepaniak, K.; Alva, V.; Dunin-Horkawicz, S.: DeepCoil: a fast and accurate prediction of coiled-coil domains in protein sequences. In BioInformatics in Torun 2019 - BIT19, p. 40. BioInformatics in Torun 2019 (BIT19), Torun, Poland, June 27, 2019 - June 29, 2019. (2019)

Ludwiczak, J.; Jarmula, A.; Dunin-Horkawicz, S.: Increasing sequence diversity in protein design by combining Rosetta with molecular dynamics. In 7th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 40. 7th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 03, 2017 - September 08, 2017. (2017)

Szczepaniak, K.; Ludwiczak, J.; Dunin-Horkawicz, S.: Fine-tuning of coiled coil design. In 7th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 18. 7th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 03, 2017 - September 08, 2017. (2017)

Martinez Goikoetxea, M.; Madaj, R.; Ludwiczak, J.; Lupas, A.; Dunin-Horkawicz, S.: Old folds can learn new tricks: Alphafold-driven insights on coiled-coil structure. 3D-BioInfo ICSB 3D-SIG ELIXIR Czech Republic Community Meeting in Structural Bioinformatics, Praha, Czech Republic (2023)

Kanhema, T.; Parobczak, K.; Patil, S.; Holm-Kaczmarek, D.; Hallin, E.; Ludwiczak, J.; Szczepankiewicz, A.; Pauzin, F.; Szum, A.; Ishizuka, Y. et al.; 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. (submitted)

Madaj, R.; Martinez-Goikoetxea, M.; Kaminski, K.; Ludwiczak, J.; Dunin-Horkawicz, S.: Applicability of AlphaFold2 in the modelling of coiled-coil domains. (submitted)