Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Biological code of knots – identification of knotted patterns in biomolecules via AI approach

2021/43/I/NZ1/03341

Keywords:

structural biology knot theory structure prediction protein folding knots lassos theta-curves

Descriptors:

  • NZ2_008:
  • NZ1_003:
  • ST1_006:

Panel:

NZ1 - Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution :

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Joanna Ida Sułkowska 

Number of co-investigators in the project: 5

Call: OPUS 22 (LAP) - announced on 2021-09-15

Amount awarded: 1 279 475 PLN

Project start date (Y-m-d): 2022-09-23

Project end date (Y-m-d): 2025-09-22

Project duration:: 36 months (the same as in the proposal)

Project status: Project completed

Project description

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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 (8)
  1. Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
    Authors:
    Bruno da Silva, F., Gabrovšek, B., Korpacz, M., Luczkiewicz, K., Niewieczerzal, S., Sikora, M., & Sulkowska, J. I.
    Academic press:
    Macromolecules (rok: 2024, tom: 57, strony: 4599−4608), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.macromol.3c02479 - link to the publication
  2. Knotted artifacts in predicted 3D RNA structures
    Authors:
    BA Gren, M Antczak, T Zok, JI Sulkowska, M Szachniuk
    Academic press:
    PLOS Computational Biology (rok: 2024, tom: 20, strony: 46038), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1011959 - link to the publication
  3. AlphaFold predicts novel human proteins with knots
    Authors:
    AP Perlinska, WH Niemyska, BA Gren, M Bukowicki, S Nowakowski, P Rubach, JI Sulkowska
    Academic press:
    Protein Science (rok: 2023, tom: 32(5), strony: 46032), Wydawca: Wiley-Blackwell
    Status:
    Published
    DOI:
    10.1002/pro.4631 - link to the publication
  4. Conservation of knotted and slipknotted topology in transmembrane transporters
    Authors:
    V Zayats, M Sikora, AP Perlinska, A Stasiulewicz, B Gren, JI Sulkowska
    Academic press:
    Biophysical Journal (rok: 2023, tom: 122(23), strony: 46032), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.031 - link to the publication
  5. Everything AlphaFold tells us about protein knots
    Authors:
    A Perlinska, M Sikora, JI Sulkowska
    Academic press:
    Journal of Molecular Biology (rok: 2024, tom: 436, strony: 46035), Wydawca: science direct
    Status:
    Published
    DOI:
    10.1016/j.jmb.2024.168715 - link to the publication
  6. Discovery of a Trefoil Knot in the RydC RNA: Challenging Previous Notions of RNA Topology
    Authors:
    W Niemyska, S Mukherjee, B Gren, S Niewieczerzal, JM Bujnicki, JI Sulkowska
    Academic press:
    Journal of Molecular Biology (rok: 2024, tom: 436, strony: 46033), Wydawca: Science Direct
    Status:
    Published
    DOI:
    10.1016/j.jmb.2024.168455 - link to the publication
  7. AlphaKnot 2.0 – a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models
    Authors:
    P Rubach, M Sikora, AI Jarmolinska, AP Perlinska, JI Sulkowska
    Academic press:
    Nucleic Acids Research (rok: 2024, tom: 52, strony: W187–W193), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkae443 - link to the publication
  8. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model
    Authors:
    D Šrámková, M Sikora, D Uchal, E Klimentová, AP Perlinska, ML Nguyen, M Korpacz, R Malinowska, P Rubach, P Šimeček, JI Sulkowska
    Academic press:
    Protein Science (rok: 2023, tom: 1, strony: 46043), Wydawca: Wiley-Blackwell
    Status:
    Published
    DOI:
    10.1002/pro.4998 - link to the publication

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