Ludwiczak J - Search Results

1

Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N(4)-hydroxy-dCMP.

Ludwiczak J, Maj P, Wilk P, Frączyk T, Ruman T, Kierdaszuk B, Jarmuła A, Rode W. Ludwiczak J, et al. Mol Biosyst. 2016 Apr;12(4):1333-41. doi: 10.1039/c6mb00026f. Epub 2016 Feb 26. Mol Biosyst. 2016. PMID: 26916840 Free article.

2

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.

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. Jarmuła A, et al. Among authors: ludwiczak j. J Mol Graph Model. 2017 Oct;77:33-50. doi: 10.1016/j.jmgm.2017.08.008. Epub 2017 Aug 12. J Mol Graph Model. 2017. PMID: 28826032

3

β-sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β-amyloid fibrils.

Jarmuła A, Ludwiczak J, Stępkowski D. Jarmuła A, et al. Among authors: ludwiczak j. Proteins. 2021 Jul;89(7):762-780. doi: 10.1002/prot.26057. Epub 2021 Feb 18. Proteins. 2021. PMID: 33550630

4

Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

Ludwiczak J, Jarmula A, Dunin-Horkawicz S. Ludwiczak J, et al. J Struct Biol. 2018 Jul;203(1):54-61. doi: 10.1016/j.jsb.2018.02.004. Epub 2018 Feb 14. J Struct Biol. 2018. PMID: 29454111

5

Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study.

Ludwiczak J, Szczęsna E, da Silva Neto AM, Cieplak P, Kasprzak AA, Jarmuła A. Ludwiczak J, et al. Biochem J. 2019 Sep 10;476(17):2449-2462. doi: 10.1042/BCJ20190484. Biochem J. 2019. PMID: 31416830

6

Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.

Banaś AM, Bocian-Ostrzycka KM, Dunin-Horkawicz S, Ludwiczak J, Wilk P, Orlikowska M, Wyszyńska A, Dąbrowska M, Plichta M, Spodzieja M, Polańska MA, Malinowska A, Jagusztyn-Krynicka EK. Banaś AM, et al. Among authors: ludwiczak j. Int J Mol Sci. 2021 Dec 15;22(24):13451. doi: 10.3390/ijms222413451. Int J Mol Sci. 2021. PMID: 34948248 Free PMC article.

7

Variability of the core geometry in parallel coiled-coil bundles.

Szczepaniak K, Ludwiczak J, Winski A, Dunin-Horkawicz S. Szczepaniak K, et al. Among authors: ludwiczak j. J Struct Biol. 2018 Oct;204(1):117-124. doi: 10.1016/j.jsb.2018.07.002. Epub 2018 Jul 2. J Struct Biol. 2018. PMID: 30042011

8

PiPred - a deep-learning method for prediction of π-helices in protein sequences.

Ludwiczak J, Winski A, da Silva Neto AM, Szczepaniak K, Alva V, Dunin-Horkawicz S. Ludwiczak J, et al. Sci Rep. 2019 May 3;9(1):6888. doi: 10.1038/s41598-019-43189-4. Sci Rep. 2019. PMID: 31053765 Free PMC article.

9

DeepCoil-a fast and accurate prediction of coiled-coil domains in protein sequences.

Ludwiczak J, Winski A, Szczepaniak K, Alva V, Dunin-Horkawicz S. Ludwiczak J, et al. Bioinformatics. 2019 Aug 15;35(16):2790-2795. doi: 10.1093/bioinformatics/bty1062. Bioinformatics. 2019. PMID: 30601942

10

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.

Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S. Kamiński K, et al. Among authors: ludwiczak j. Brief Bioinform. 2022 Jan 17;23(1):bbab371. doi: 10.1093/bib/bbab371. Brief Bioinform. 2022. PMID: 34571541 Free PMC article.

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