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Laboratory of Structural Bioinformatics


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)
  • Development and validation of bioinformatic tools for high-throughput structure analysis of coiled-coil domains, with particular emphasis on the AlphaFold2 method (IDUB BOB-IDUB-622-314/2022)

Computational resources

Theses in progress

  • Kamil Pawlicki, “Application of different language model architectures to the task of protein sequence classification“, Master’s thesis, Faculty of Biology

Completed theses

  • Julia Gołębiowska, „Predicting absorption wavelengths of rhodopsins using machine learning-based methods”, Master’s thesis, Faculty of Mathematics, Informatics and Mechanics (supervised also by Anna Karnkowska, PhD, Faculty of Biology)
  • Kamil Kamiński, „Re-engineering cofactor specificity of the Rossmann fold proteins using graph neural networks”, 2020, Master’s thesis, Faculty of Physics
  • Adriana Bukała, „Ancestral state reconstruction approach in investigating Rossmann fold evolution”, 2020, bachelor thesis, Faculty of Mathematics, Informatics and Mechanics
  • Aleksander Wiński, „The use of deep learning methods to predict protein π helix secondary structure based on sequence and evolutionary information”, 2018, bachelor thesis, Faculty of Physics
  • Bartosz Szymański, „Modelling and substrate spectra characteristics  of laccase from Trametes versicolor”, Bachelor’s thesis, IISMNS
  • Jędrzej Kubica, “Sequence analysis and structure modeling of bacterial receptor proteins of unknown function“, Master’s thesis, Department of Chemistry (supervised also by prof. Dominik Gront, Department of Chemistry)

Selected publications

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

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; 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

Szustak, Marcin; Korkus, Eliza; Madaj, Rafal; Chworos, Arkadiusz; Dąbrowski, Grzegorz; Czaplicki, Sylwester; Tabandeh, Erfan; Maciejewska, Gabriela; Koziołkiewicz, Maria; Konopka, Iwona; Gliszczyńska, Anna; Gendaszewska-Darmach, Edyta

Lysophosphatidylcholines Enriched with cis and trans Palmitoleic Acid Regulate Insulin Secretion via GPR119 Receptor Journal Article

In: ACS Medicinal Chemistry Letters, vol. 0, no. 0, pp. null, 0000.

Links | BibTeX