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Laboratory of Structural Bioinformatics

Research

The amount of available biological data, originating from various experimental procedures (genome and transcriptome sequencing, structure determination, functional assays), is vast. In our group, we employ computational techniques, such as deep learning, molecular dynamics simulations, and sequence analysis to make use of this data. We are particularly interested in understanding how protein folds have emerged and how protein structures and functions are encoded by the alphabet of 20 amino acids.

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)

Computational resources

Selected publications

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

Szczupak, Patrycja; Radzikowska-Cieciura, Ewa; Kulik, Katarzyna; Madaj, Rafał; Sierant, Małgorzata; Krakowiak, Agnieszka; Nawrot, Barbara

Escherichia coli tRNA 2-selenouridine synthase SelU selects its prenyl substrate to accomplish its enzymatic function Journal Article

Bioorganic Chemistry, 122 , pp. 105739, 2022, ISSN: 00452068.

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

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; 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