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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Design of new protein structures with precisely defined features using parametric models.

2015/18/E/NZ1/00689

Keywords:

proteins structure bioinformatics design parameterization coiled coils beta-helix

Descriptors:

  • NZ1_4: Structural biology
  • NZ2_7: Bioinformatics

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 Stanisław Dunin-Horkawicz 

Number of co-investigators in the project: 3

Call: SONATA BIS 5 - announced on 2015-06-15

Amount awarded: 1 064 040 PLN

Project start date (Y-m-d): 2016-06-08

Project end date (Y-m-d): 2019-12-07

Project duration:: 42 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. Oprogramowanie AMBER.
  2. Dodatkowy węzeł do klastra obliczeniowego.
  3. Komputer osobisty (3 szt.) (24 000 PLN)
  4. Oprogramowanie biurowe (600 PLN)
  5. Węzły do klastra obliczeniowego (3 szt.) (75 000 PLN)

Information in the final report

  • Publication in academic press/journals (7)
  1. Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design
    Authors:
    Jan Ludwiczak, Adam Jarmula, Stanislaw Dunin-Horkawicz
    Academic press:
    Journal of Structural Biology (rok: 2018, tom: 203, strony: 54-61), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jsb.2018.02.004 - link to the publication
  2. A library of coiled-coil domains: from regular bundles to peculiar twists
    Authors:
    Krzysztof Szczepaniak, Adriana Bukala, Antonio Marinho da Silva Neto, Jan Ludwiczak, Stanislaw Dunin-Horkawicz
    Academic press:
    Bioinformatics (rok: 2020, tom: nd, strony: nd), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa1041 - link to the publication
  3. DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences
    Authors:
    Jan Ludwiczak, Aleksander Winski, Krzysztof Szczepaniak, Vikram Alva, Stanisław Dunin-Horkawicz
    Academic press:
    Bioinformatics (rok: 2019, tom: 2019, strony: nie dotyczy), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty1062 - link to the publication
  4. RRMdb-an evolutionary-oriented database of RNA recognition motif sequences
    Authors:
    Martyna Nowacka, Pietro Boccaletto, Elżbieta Jankowska, Tomasz Jarzynka, Janusz Bujnicki, Stanisław Dunin-Horkawicz
    Academic press:
    Database (Oxford) (rok: 2019, tom: 2019, strony: 45296), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/database/bay148 - link to the publication
  5. Self-analysis of repeat proteins reveals evolutionarily conserved patterns
    Authors:
    Matthew Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz, Maria W. Gorna
    Academic press:
    BMC Bioinformatics (rok: 2020, tom: 7;21(1):179, strony: nd), Wydawca: BioMed Central
    Status:
    Accepted for publication
    DOI:
    10.1186/s12859-020-3493-y - link to the publication
  6. Variability of the core geometry in parallel coiled-coil bundles
    Authors:
    Krzysztof Szczepaniak, Jan Ludwiczak, Aleksander Winski, Stanislaw Dunin- Horkawicz
    Academic press:
    Journal of Structural Biology (rok: 2018, tom: 204, strony: 117-124), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jsb.2018.07.002 - link to the publication
  7. PiPred – a deep-learning method for prediction of π-helices in protein sequences
    Authors:
    Aleksander Winski, Jan Ludwiczak, Vikram Alva, Antonio Marinho da Silva Neto, Krzysztof Szczepaniak, Stanislaw Dunin-Horkawicz
    Academic press:
    Scientific Reports (rok: 2019, tom: 9, strony: 6888), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-019-43189-4 - link to the publication

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