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dr Stanisław Dunin-Horkawicz

Zainteresowania badawcze

Prowadzone przeze mnie badania dotyczą rozwoju i zastosowania metod obliczeniowych w celu lepszego zrozumienia zależności pomiędzy sekwencją, strukturą i funkcją białek. W szczególności interesują mnie zagadnienia związane z wykorzystaniem metod uczenia maszynowego w badaniu sekwencji i struktur białkowych, pochodzeniem najstarszych rodzin białkowych, funkcją i strukturą białek włóknistych (w szczególności wiązek splecionych helis).

Dydaktyka

  • Bioinformatyka praktyczna

Aktualnie realizowane projekty badawcze

  • Zastosowanie metod biologii systemowej w celu zrozumienia ewolucji i roli ścieżek molekularnych powiązanych z wielokomórkowością (NCN OPUS 2020/37/B/NZ2/03268)

Wybrane publikacje

Winski, Aleksander; Ludwiczak, Jan; Orlowska, Malgorzata; Madaj, Rafal; Kaminski, Kamil; Dunin-Horkawicz, Stanislaw

AlphaFold2 captures the conformational landscape of the HAMP signaling domain Journal Article

In: Protein Science, vol. 33, no. 1, pp. e4846, 2024.

Abstract | Links | BibTeX

Smug, Bogna J.; Szczepaniak, Krzysztof; Rocha, Eduardo P. C.; Dunin-Horkawicz, Stanislaw; Mostowy, Rafał J.

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts Journal Article

In: Nature Communications, vol. 14, no. 1, pp. 7460, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

Kaminski, Kamil; Ludwiczak, Jan; Pawlicki, Kamil; Alva, Vikram; Dunin-Horkawicz, Stanislaw

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models Journal Article

In: Bioinformatics, vol. 39, no. 10, pp. btad579, 2023, ISSN: 1367-4811.

Abstract | Links | BibTeX

Ludwiczak, Jan; Winski, Aleksander; Dunin-Horkawicz, Stanislaw

localpdb —a Python package to manage protein structures and their annotations Journal Article

In: Bioinformatics, 2022, ISSN: 1367-4803.

Abstract | Links | BibTeX

Kamiński, Kamil; Ludwiczak, Jan; Jasiński, Maciej; Bukala, Adriana; Madaj, Rafal; Szczepaniak, Krzysztof; Dunin-Horkawicz, Stanisław

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins Journal Article

In: Briefings in Bioinformatics, vol. 23, 2022, ISSN: 1467-5463.

Abstract | Links | BibTeX

Latoszek, Ewelina; Wiweger, Małgorzata; Ludwiczak, Jan; Dunin-Horkawicz, Stanisław; Kuznicki, Jacek; Czeredys, Magdalena

Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models Journal Article

In: Cell & Bioscience, vol. 12, pp. 34, 2022, ISSN: 2045-3701.

Abstract | Links | BibTeX

Szczepaniak, Krzysztof; Bukala, Adriana; da Neto, Antonio Marinho Silva; Ludwiczak, Jan; Dunin-Horkawicz, Stanislaw

A library of coiled-coil domains: from regular bundles to peculiar twists Journal Article

In: Bioinformatics, vol. 36, pp. 5368-5376, 2021, ISSN: 1367-4803.

Abstract | Links | BibTeX

Banaś, Anna M; Bocian-Ostrzycka, Katarzyna M; Dunin-Horkawicz, Stanisław; Ludwiczak, Jan; Wilk, Piotr; Orlikowska, Marta; Wyszyńska, Agnieszka; Dąbrowska, Maria; Plichta, Maciej; Spodzieja, Marta; Polańska, Marta A; Malinowska, Agata; Jagusztyn-Krynicka, Elżbieta Katarzyna

Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis Journal Article

In: International Journal of Molecular Sciences, vol. 22, pp. 13451, 2021, ISSN: 1422-0067.

Abstract | Links | BibTeX

Adamczyk, M; Lewicka, E; Szatkowska, R; Nieznanska, H; Ludwiczak, J; Jasiński, M; Dunin-Horkawicz, S; Sitkiewicz, E; Swiderska, B; Goch, G; Jagura-Burdzy, G

Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins Journal Article

In: BMC Microbiology, vol. 21, pp. 32, 2021, ISSN: 1471-2180.

Abstract | Links | BibTeX

Zayats, Vasilina; Perlinska, Agata P; Jarmolinska, Aleksandra; Jastrzebski, Borys; Dunin-Horkawicz, Stanislaw; Sulkowska, Joanna

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor Journal Article

In: PLOS Computational Biology, vol. 17, pp. e1009502, 2021, ISSN: 1553-7358.

Abstract | Links | BibTeX

Banaś, Anna Marta; Bocian-Ostrzycka, Katarzyna Marta; Plichta, Maciej; Dunin-Horkawicz, Stanisław; Ludwiczak, Jan; Płaczkiewicz, Jagoda; Jagusztyn-Krynicka, Elżbieta Katarzyna

C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning Journal Article

In: PLOS ONE, vol. 15, pp. e0230366, 2020, ISSN: 1932-6203.

Abstract | Links | BibTeX

Ludwiczak, Jan; Winski, Aleksander; Szczepaniak, Krzysztof; Alva, Vikram; Dunin-Horkawicz, Stanislaw

DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences Journal Article

In: Bioinformatics, vol. 35, pp. 2790-2795, 2019, ISSN: 1367-4803.

Abstract | Links | BibTeX

Nowacka, Martyna; Boccaletto, Pietro; Jankowska, Elzbieta; Jarzynka, Tomasz; Bujnicki, Janusz M; Dunin-Horkawicz, Stanislaw

RRMdb—an evolutionary-oriented database of RNA recognition motif sequences Journal Article

In: Database, vol. 2019, 2019, ISSN: 1758-0463.

Abstract | Links | BibTeX

Ludwiczak, Jan; Winski, Aleksander; da Neto, Antonio Marinho Silva; Szczepaniak, Krzysztof; Alva, Vikram; Dunin-Horkawicz, Stanislaw

PiPred – a deep-learning method for prediction of π-helices in protein sequences Journal Article

In: Scientific Reports, vol. 9, pp. 6888, 2019, ISSN: 2045-2322.

Links | BibTeX

Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design Journal Article

In: Journal of Structural Biology, vol. 203, pp. 54-61, 2018, ISSN: 10478477.

Abstract | Links | BibTeX

Szczepaniak, Krzysztof; Ludwiczak, Jan; Winski, Aleksander; Dunin-Horkawicz, Stanislaw

Variability of the core geometry in parallel coiled-coil bundles Journal Article

In: Journal of Structural Biology, vol. 204, pp. 117-124, 2018, ISSN: 10478477.

Abstract | Links | BibTeX

Dunin-Horkawicz, Stanislaw; Kopec, Klaus O; Lupas, Andrei N

Prokaryotic Ancestry of Eukaryotic Protein Networks Mediating Innate Immunity and Apoptosis Journal Article

In: Journal of Molecular Biology, vol. 426, pp. 1568-1582, 2014, ISSN: 00222836.

Abstract | Links | BibTeX

Majorek, Karolina A; Dunin-Horkawicz, Stanislaw; Steczkiewicz, Kamil; Muszewska, Anna; Nowotny, Marcin; Ginalski, Krzysztof; Bujnicki, Janusz M

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification Journal Article

In: Nucleic Acids Research, vol. 42, pp. 4160-4179, 2014, ISSN: 1362-4962.

Abstract | Links | BibTeX

Dunin-Horkawicz, Stanislaw; Lupas, Andrei N

Comprehensive Analysis of HAMP Domains: Implications for Transmembrane Signal Transduction Journal Article

In: Journal of Molecular Biology, vol. 397, pp. 1156-1174, 2010, ISSN: 00222836.

Abstract | Links | BibTeX

Dunin-Horkawicz, Stanislaw; Lupas, Andrei N

Measuring the conformational space of square four-helical bundles with the program samCC Journal Article

In: Journal of Structural Biology, vol. 170, pp. 226-235, 2010, ISSN: 10478477.

Abstract | Links | BibTeX

Dunin-Horkawicz, S

MODOMICS: a database of RNA modification pathways Journal Article

In: Nucleic Acids Research, vol. 34, pp. D145-D149, 2006, ISSN: 0305-1048.

Abstract | Links | BibTeX

Dunin-Horkawicz, Stanislaw; Feder, Marcin; Bujnicki, Janusz M

Phylogenomic analysis of the GIY-YIG nuclease superfamily Journal Article

In: BMC Genomics, vol. 7, pp. 98, 2006, ISSN: 1471-2164.

Abstract | Links | BibTeX