Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Identification and characterization of proteins with link topology

2016/21/N/NZ1/02848

Keywords:

proteins topology links knots simulations

Descriptors:

  • NZ1_3: Biophysics
  • NZ1_4: Structural biology
  • ST1_6: Topology

Panel:

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

Host institution :

Uniwersytet Warszawski, Wydział Chemii

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

Paweł Dąbrowski-Tumański 

Number of co-investigators in the project: 3

Call: PRELUDIUM 11 - announced on 2016-03-15

Amount awarded: 100 000 PLN

Project start date (Y-m-d): 2017-01-24

Project end date (Y-m-d): 2019-10-23

Project duration:: 33 months (the same as in the proposal)

Project status: Project settled

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.

Equipment purchased [PL]

  1. Serwer obliczeniowy (22 000 PLN)

Information in the final report

  • Publication in academic press/journals (9)
  1. Genus trace reveals the topological complexity and domain structure of biomolecules
    Authors:
    Zajac S, Geary C, Andersen ES, Dabrowski-Tumanski P, Sulkowska JI, Sułkowski P
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 17537), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-018-35557-3 - link to the publication
  2. KnotProt 2.0: a database of proteins with knots and other entangled structures
    Authors:
    Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sułkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 47, strony: D367-D375), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky1140 - link to the publication
  3. To Tie or Not to Tie? That Is the Question
    Authors:
    Pawel Dabrowski-Tumanski, Joanna I. Sulkowska
    Academic press:
    Polymers (rok: 2017, tom: 9, strony: 454), Wydawca: Multidisciplinary Digital Publishing Institute
    Status:
    Published
    DOI:
    10.3390/polym9090454 - link to the publication
  4. PyLink: a PyMOL plugin to identify links
    Authors:
    Gierut A, Dabrowski-Tumanski P, Niemyska W, Millett KC, Sulkowska JI
    Academic press:
    Bioinformatics (rok: 2019, tom: bty1038, strony: bty1038), Wydawca: Oxford University Press}
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty1038 - link to the publication
  5. GapRepairer–a server to model a structural gap and validate it using topological analysis
    Authors:
    Jarmolinska AI, Kadlof M, Dabrowski-Tumanski P, Sulkowska JI
    Academic press:
    Bioinformatics (rok: 2018, tom: 34, strony: 3300-3307), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty334 - link to the publication
  6. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting From the Ribosome Exit Channel
    Authors:
    Dabrowski-Tumanski P, Piejko M, Niewieczerzal S, Stasiak A, Sulkowska JI
    Academic press:
    Journal of Physical Chemistry B (rok: 2018, tom: 122, strony: 11616-11625), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.8b07634 - link to the publication
  7. PyLasso: a PyMOL plugin to identify lassos
    Authors:
    Aleksandra M Gierut, Wanda Niemyska, Pawel Dabrowski-Tumanski, Piotr Sułkowski, Joanna I Sulkowska
    Academic press:
    Bioinformatics (rok: 2017, tom: 33, strony: 3819–3821), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btx493 - link to the publication
  8. Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function
    Authors:
    Pawel, Dabrowski-Tumanski, Bartosz Gren, Joanna I Sulkowska
    Academic press:
    Polymers (rok: 2019, tom: 11, strony: 707), Wydawca: MDPI, ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND
    Status:
    Published
    DOI:
    10.3390/polym11040707 - link to the publication
  9. The exclusive effects of chaperonin on the behavior of proteins with 52 knot
    Authors:
    Zhao Y, Dabrowski-Tumanski P, Niewieczerzal S, Sulkowska JI
    Academic press:
    PLoS Computational Biology (rok: 2018, tom: 14, strony: e1005970), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1005970 - link to the publication

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