Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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UNDERSTANDING CROSS-TALK BETWEEN AMYLOID PROTEINS

2019/35/B/NZ2/03997

Keywords:

amyloid bioinformatic modeling inter-molecular contacts machine learning molecular dynamics spectroscopy ATR-FTiR AFM microscopy data base

Descriptors:

  • NZ2_007:
  • NZ2_003:
  • NZ2_010:

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Politechnika Wrocławska

woj. dolnośląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Małgorzata Kotulska 

Number of co-investigators in the project: 6

Call: OPUS 18 - announced on 2019-09-16

Amount awarded: 1 523 280 PLN

Project start date (Y-m-d): 2020-09-01

Project end date (Y-m-d): 2025-08-31

Project duration:: 60 months (the same as in the proposal)

Project status: Project completed

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (20)
  • Book publications / chapters in book publications (4)
  1. Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild-type rats
    Authors:
    Christensen LFB, Alijanvand SH, Burdukiewicz M, Herbst FA, Kjeldal H, Dueholm MS, Otzen DE
    Academic press:
    Protein Science (rok: 2021, tom: 30, strony: 1854-1870), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.4137 - link to the publication
  2. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
    Authors:
    Dyrka W, Gąsior-Głogowska M, Szefczyk M, Szulc N.
    Academic press:
    BMC Bioinformatics (rok: 2021, tom: 22, strony: 222), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-021-04139-y - link to the publication
  3. Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild-type rats
    Authors:
    Christensen LFB, Alijanvand SH, Burdukiewicz M, Herbst FA, Kjeldal H, Dueholm MS, Otzen DE
    Academic press:
    Protein Science (rok: 2021, tom: 30, strony: 1854-1870), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.4137 - link to the publication
  4. AmyloGraph: a comprehensive database of amyloid-amyloid interactions
    Authors:
    Burdukiewicz M, Rafacz D, Barbach A, Hubicka K, Bąkała L, Lassota A, Stecko J, Szymańska N, Wojciechowski JW, Kozakiewicz D, Szulc N, Chilimoniuk J, Jęśkowiak I, Gąsior-Głogowska M, Kotulska M.
    Academic press:
    Nucleic Acid Research (rok: 2022, tom: 51, strony: D352–D357), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkac882 - link to the publication
  5. Topological analysis as a tool for detection of abnormalities in protein-protein interaction data
    Authors:
    Nowakowska AW, Kotulska M
    Academic press:
    Bioinformatics (rok: 2022, tom: 38 (21), strony: 4997), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac440 - link to the publication
  6. Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli
    Authors:
    Szulc N, Gąsior-Głogowska M, Wojciechowski JW, Szefczyk M, Żak AM, Burdukiewicz M, Kotulska M.
    Academic press:
    International Journal of Molecular Science (rok: 2021, tom: 22, strony: 5127), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22105127 - link to the publication
  7. Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli
    Authors:
    Szulc N, Gąsior-Głogowska M, Wojciechowski JW, Szefczyk M, Żak AM, Burdukiewicz M, Kotulska M.
    Academic press:
    International Journal of Molecular Science (rok: 2021, tom: 22, strony: 5127), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22105127 - link to the publication
  8. Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data
    Authors:
    Szulc N, Burdukiewicz M, Gąsior-Głogowska M, Wojciechowski JW, Chilimoniuk J, Mackiewicz P, Šneideris T, Smirnovas V, Kotulska M.
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 8934), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-021-86530-6 - link to the publication
  9. AmyloGraph: a comprehensive database of amyloid-amyloid interactions
    Authors:
    Burdukiewicz M, Rafacz D, Barbach A, Hubicka K, Bąkała L, Lassota A, Stecko J, Szymańska N, Wojciechowski JW, Kozakiewicz D, Szulc N, Chilimoniuk J, Jęśkowiak I, Gąsior-Głogowska M, Kotulska M.
    Academic press:
    Nucleic Acid Research (rok: 2022, tom: 51, strony: D352–D357), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkac882 - link to the publication
  10. Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data
    Authors:
    Szulc N, Burdukiewicz M, Gąsior-Głogowska M, Wojciechowski JW, Chilimoniuk J, Mackiewicz P, Šneideris T, Smirnovas V, Kotulska M.
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 8934), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-021-86530-6 - link to the publication
  11. Topological analysis as a tool for detection of abnormalities in protein-protein interaction data
    Authors:
    Nowakowska AW, Kotulska M
    Academic press:
    Bioinformatics (rok: 2022, tom: 38 (21), strony: 4997), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac440 - link to the publication
  12. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins
    Authors:
    Muntasir Kamal, Levon Tokmakjian, Jessica Knox, Peter Mastrangelo, Jingxiu Ji, Hao Cai, Jakub W Wojciechowski, Michael P Hughes, Kristóf Takács, Xiaoquan Chu, Jianfeng Pei, Vince Grolmusz, Malgorzata Kotulska, Julie Deborah Forman-Kay, Peter J Roy
    Academic press:
    eLife (rok: 2022, tom: 11, strony: e79396), Wydawca: eLife
    Status:
    Published
    DOI:
    10.7554/eLife.79396 - link to the publication
  13. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
    Authors:
    Dyrka W, Gąsior-Głogowska M, Szefczyk M, Szulc N.
    Academic press:
    BMC Bioinformatics (rok: 2021, tom: 22, strony: 222), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-021-04139-y - link to the publication
  14. Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild-type rats
    Authors:
    Christensen LFB, Alijanvand SH, Burdukiewicz M, Herbst FA, Kjeldal H, Dueholm MS, Otzen DE
    Academic press:
    Protein Science (rok: 2021, tom: 30, strony: 1854-1870), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.4137 - link to the publication
  15. The role of tandem repeats in bacterial functional amyloids
    Authors:
    Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M.
    Academic press:
    Journal of Structural Biology (rok: 2023, tom: 215(3), strony: 108002), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jsb.2023.108002 - link to the publication
  16. PACT - Prediction of amyloid cross-interaction by threading
    Authors:
    Wojciechowski JW, Szczurek W, Szulc N, Szefczyk M, Kotulska M
    Academic press:
    Scientific Reports (rok: 2023, tom: 13, strony: 22268), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-023-48886-9 - link to the publication
  17. Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data
    Authors:
    Szulc N, Burdukiewicz M, Gąsior-Głogowska M, Wojciechowski JW, Chilimoniuk J, Mackiewicz P, Šneideris T, Smirnovas V, Kotulska M.
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 8934), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-021-86530-6 - link to the publication
  18. Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli
    Authors:
    Szulc N, Gąsior-Głogowska M, Wojciechowski JW, Szefczyk M, Żak AM, Burdukiewicz M, Kotulska M.
    Academic press:
    International Journal of Molecular Science (rok: 2021, tom: 22, strony: 5127), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22105127 - link to the publication
  19. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
    Authors:
    Dyrka W, Gąsior-Głogowska M, Szefczyk M, Szulc N.
    Academic press:
    BMC Bioinformatics (rok: 2021, tom: 22, strony: 222), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-021-04139-y - link to the publication
  20. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins
    Authors:
    Muntasir Kamal, Levon Tokmakjian, Jessica Knox, Peter Mastrangelo, Jingxiu Ji, Hao Cai, Jakub W Wojciechowski, Michael P Hughes, Kristóf Takács, Xiaoquan Chu, Jianfeng Pei, Vince Grolmusz, Malgorzata Kotulska, Julie Deborah Forman-Kay, Peter J Roy
    Academic press:
    eLife (rok: 2022, tom: 11, strony: e79396), Wydawca: eLife
    Status:
    Published
    DOI:
    10.7554/eLife.79396 - link to the publication
  1. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins
    Authors:
    Kotulska M, Wojciechowski JW
    Book:
    Methods in Molecular Biology: Computer Simulations of Aggregation of Proteins and Peptides (rok: 2022, tom: 2340, strony: 45672), Wydawca: Humana (Springer Nature)
    Status:
    Published
    DOI:
    10.1007/978-1-0716-1546-1_1 - link to the publication
  2. Challenges in Experimental Methods
    Authors:
    Gąsior-Głogowska ME, Szulc N, Szefczyk M
    Book:
    Methods in Molecular Biology: Computer Simulations of Aggregation of Proteins and Peptides (rok: 2022, tom: 2340, strony: 281-307), Wydawca: Humana
    Status:
    Published
    DOI:
    10.1007/978-1-0716-1546-1_13 - link to the publication
  3. Challenges in Experimental Methods
    Authors:
    Gąsior-Głogowska ME, Szulc N, Szefczyk M
    Book:
    Methods in Molecular Biology: Computer Simulations of Aggregation of Proteins and Peptides (rok: 2022, tom: 2340, strony: 281-307), Wydawca: Humana
    Status:
    Published
    DOI:
    10.1007/978-1-0716-1546-1_13 - link to the publication
  4. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins
    Authors:
    Kotulska M, Wojciechowski JW
    Book:
    Methods in Molecular Biology: Computer Simulations of Aggregation of Proteins and Peptides (rok: 2022, tom: 2340, strony: 45672), Wydawca: Humana (Springer Nature)
    Status:
    Published
    DOI:
    10.1007/978-1-0716-1546-1_1 - link to the publication

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