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dr Jan Ludwiczak

Research Interests

  • Structural bioinformatics and protein modelling with emphasis on machine learning, simulation and design techniques
  • Development of bioinformatics methods and scientific software

Research projects

  • Molecular mechanisms of the allosteric communication in thymidylate synthase, National Science Centre Grant “Preludium”, 2017/27/N/NZ1/00716
  • Application of machine learning and simulation techniques to study the sequence-structure-function relationships in proteins, National Science Centre Grant “Etiuda”, 2019/32/T/NZ1/00323

Internships

  • June – December 2020: Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tuebigen, Germany

Distinctions

  • Scholarship from the President of Polish Academy of Sciences for scientific achievements (academic year 2019/2020)

Publikacje

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

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

Jarmuła, Adam; Ludwiczak, Jan; Stępkowski, Dariusz

β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils Journal Article

Proteins: Structure, Function, and Bioinformatics, 89 , pp. 762-780, 2021, ISSN: 0887-3585.

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

Ludwiczak, Jan; Szczęsna, Ewa; da Neto, Antônio Marinho Silva; Cieplak, Piotr; Kasprzak, Andrzej A; Jarmuła, Adam

Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study Journal Article

Biochemical Journal, 476 , pp. 2449-2462, 2019, ISSN: 0264-6021.

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

Jarmuła, Adam; Wilk, Piotr; Maj, Piotr; Ludwiczak, Jan; Dowierciał, Anna; Banaszak, Katarzyna; Rypniewski, Wojciech; Cieśla, Joanna; Dąbrowska, Magdalena; Frączyk, Tomasz; Bronowska, Agnieszka K; Jakowiecki, Jakub; Filipek, Sławomir; Rode, Wojciech

Crystal structures of nematode (parasitic T. spiralis and free living C. elegans ), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS Journal Article

Journal of Molecular Graphics and Modelling, 77 , pp. 33-50, 2017, ISSN: 10933263.

Abstract | Links | BibTeX

Ludwiczak, Jan; Maj, Piotr; Wilk, Piotr; Frączyk, Tomasz; Ruman, Tomasz; Kierdaszuk, Borys; Jarmuła, Adam; Rode, Wojciech

Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N 4 -hydroxy-dCMP Journal Article

Molecular BioSystems, 12 , pp. 1333-1341, 2016, ISSN: 1742-206X.

Abstract | Links | BibTeX