Publications

List of publications by Jan Ludwiczak:

Madaj R, Martinez-Goikoetxea M, Kamiński K, Ludwiczak J, Dunin-Horkawicz S
Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.
Protein Sci., 2025, Jan;34(1)
[PubMed]

Wiński A, Ludwiczak J, Orłowska M, Madaj R, Kamiński K, Dunin-Horkawicz S
AlphaFold2 captures the conformational landscape of the HAMP signaling domain.
Protein Sci., 2024, Jan;33(1)
[PubMed]

Kamiński K, Ludwiczak J, Pawlicki K, Alva V, Dunin-Horkawicz S
pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.
Bioinformatics., 2023, Oct 3;39(10)
[PubMed]

Ludwiczak J, Wiński A, Marinho A, Szczepaniak K, Alva V, Dunin-Horkawicz S
PiPred - a deep-learning method for prediction of π-helices in protein sequences.
Sci Rep., 2019, May 3;9(1):6888
[PubMed]

Ludwiczak J, Wiński A, Szczepaniak K, Alva V, Dunin-Horkawicz S
DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences.
Bioinformatics., 2019, Jan 2
[PubMed]

Ludwiczak J, Jarmula A, Dunin-Horkawicz S
Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.
J Struct Biol., 2018, Jul;203(1):54-61
[PubMed]

Ludwiczak J, Maj P, Wilk P, Frączyk T, Ruman T, Kierdaszuk B, Jarmuła A, Rode W
Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N(4)-hydroxy-dCMP.
Mol Biosyst., 2016, Apr;12(4):1333-41
[PubMed]

Ludwiczak J, Wiński A, Dunin-Horkawicz S
localpdb—a Python package to manage protein structures and their annotations.
Bioinformatics., 2022, Apr 28;38(9):2633–5
[PubMed]

Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S
Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.
Brief Bioinform., 2022, Jan 17;23(1)
[PubMed]

Szczepaniak K, Bukala A, da Silva Neto AM, Ludwiczak J, Dunin-Horkawicz S
A library of coiled-coil domains: from regular bundles to peculiar twists.
Bioinformatics., 2021, Apr 1;36(22-23):5368-5376
[PubMed]

Merski M, Młynarczyk K, Ludwiczak J, Skrzeczkowski J, Dunin-Horkawicz S, Górna MW
Self-analysis of repeat proteins reveals evolutionarily conserved patterns.
BMC Bioinformatics., 2020, May 7;21(1):179
[PubMed]

Szczepaniak K, Ludwiczak J, Wiński A, Dunin-Horkawicz S
Variability of the core geometry in parallel coiled-coil bundles.
J Struct Biol., 2018, Oct;204(1):117-124
[PubMed]

Berdyński M, Ludwiczak J, Barczak A, Barcikowska-Kotowicz M, Kuźma-Kozakiewicz M, Dunin-Horkawicz S, et al.
TREM2 Gene Compound Heterozygosity in Neurodegenerative Disorders.
J Alzheimers Dis., 2022, 89(4):1211–9
[PubMed]

Latoszek E, Wiweger M, Ludwiczak J, Dunin-Horkawicz S, Kuznicki J, Czeredys M
Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models.
Cell Biosci., 2022, Mar 19;12(1)
[PubMed]

Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S
Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins.
BMC Microbiol., 2021, Jan 22;21(1):32
[PubMed]

Jarmuła A, Ludwiczak J, Stępkowski D
β-sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β-amyloid fibrils.
Proteins., 2021, Jul;89(7):762–80
[PubMed]

Banaś AM, Bocian-Ostrzycka KM, Dunin-Horkawicz S, Ludwiczak J, Wilk P, Orlikowska M, et al.
Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.
Int J Mol Sci., 2021, Dec 15;22(24)
[PubMed]

Banaś AM, Bocian-Ostrzycka KM, Plichta M, Dunin-Horkawicz S, Ludwiczak J, Płaczkiewicz J, et al.
C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning.
PLoS One., 2020, 15(3):e0230366
[PubMed]

Ludwiczak J, Szczęsna E, da Silva Neto AM, Cieplak P, Kasprzak AA, Jarmuła A
Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study.
Biochem J., 2019, Sep 10;476(17):2449–62
[PubMed]

Jarmuła A, Wilk P, Maj P, Ludwiczak J, Dowierciał A, Banaszak K, Rypniewski W, Cieśla J, Dąbrowska M, Frączyk T, Bronowska AK, Jakowiecki J, Filipek S, Rode W
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.
J Mol Graph Model., 2017, Oct;77:33-50
[PubMed]