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dr Stanisław Dunin-Horkawicz

Research Interests

My research involves the development and application of computational methods to understand the relationships between sequences, structures and functions of proteins. In particular, I am interested in topics related to (i) the use of machine learning methods in the study of protein sequences and structures, (ii) the origin of the oldest protein families, and (iii) the function and structure of fibrious proteins (in particular coiled-coil domains).

Didactics

  • Practical Bioinformatics

Research projects

  • A systems biology approach to study the role and evolution of molecular pathways related to multicellularity (NCN OPUS 2020/37/B/NZ2/03268)

Publications review

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

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

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

Briefings in Bioinformatics, 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

Cell & Bioscience, 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

Bioinformatics, 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

International Journal of Molecular Sciences, 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

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

Abstract | Links | BibTeX

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

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

PLOS Computational Biology, 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

PLOS ONE, 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

Bioinformatics, 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

Database, 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

Scientific Reports, 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

Journal of Structural Biology, 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

Journal of Structural Biology, 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

Journal of Molecular Biology, 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

Nucleic Acids Research, 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

Journal of Molecular Biology, 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

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

Abstract | Links | BibTeX

Dunin-Horkawicz, S

MODOMICS: a database of RNA modification pathways Journal Article

Nucleic Acids Research, 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

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

Abstract | Links | BibTeX