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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Feature exploration and modelling of quadruplex structures

2019/35/B/ST6/03074

Keywords:

combinatorial algorithm database web application visualization neural networks classification structure modelling structural parameters 3D structure quadruplex tetrad nucleic acid

Descriptors:

  • ST6_013:
  • ST6_012:

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Politechnika Poznańska, Wydział Informatyki i Telekomunikacji

woj. wielkopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Marta Xymena Szachniuk 

Number of co-investigators in the project: 7

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

Amount awarded: 867 600 PLN

Project start date (Y-m-d): 2020-07-14

Project end date (Y-m-d): 2023-07-13

Project duration:: 36 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.

Information in the final report

  • Publication in academic press/journals (32)
  1. RNAloops: a database of RNA multiloops
    Authors:
    J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 4200–4205), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac484 - link to the publication
  2. How bioinformatics resources work with G4 RNAs
    Authors:
    J. Miskiewicz, J. Sarzynska, M. Szachniuk
    Academic press:
    Briefings in Bioinformatics (rok: 2021, tom: 22, strony: 45671), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bib/bbaa201 - link to the publication
  3. Virxicon: a lexicon of viral sequences
    Authors:
    M. Kudla, K. Gutowska, J. Synak, M. Weber, K.S. Bohnsack, P. Lukasiak, T. Villmann, J. Blazewicz, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2020, tom: 36, strony: 5507-5513), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa1066 - link to the publication
  4. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
    Authors:
    F. Carrascoza, M. Antczak, Z. Miao, E. Westhof, M. Szachniuk
    Academic press:
    RNA (rok: 2022, tom: 28, strony: 250-262), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1261/rna.078685.121 - link to the publication
  5. Entanglements of structure elements revealed in RNA 3D models
    Authors:
    M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2021, tom: 49, strony: 9625-9632), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab716 - link to the publication
  6. ONQUADRO: a database of experimentally determined quadruplex structures
    Authors:
    T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: D253-D258), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab1118 - link to the publication
  7. RNAloops: a database of RNA multiloops
    Authors:
    J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 4200–4205), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac484 - link to the publication
  8. ONQUADRO: a database of experimentally determined quadruplex structures
    Authors:
    T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: D253-D258), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab1118 - link to the publication
  9. In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients
    Authors:
    T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski
    Academic press:
    Applied Sciences (rok: 2020, tom: 10, strony: 7275), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/app10207275 - link to the publication
  10. RNAspider: a webserver to analyze entanglements in RNA 3D structures
    Authors:
    K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: W663-W669), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac218 - link to the publication
  11. Entanglements of structure elements revealed in RNA 3D models
    Authors:
    M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2021, tom: 49, strony: 9625-9632), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab716 - link to the publication
  12. Virxicon: a lexicon of viral sequences
    Authors:
    M. Kudla, K. Gutowska, J. Synak, M. Weber, K.S. Bohnsack, P. Lukasiak, T. Villmann, J. Blazewicz, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2020, tom: 36, strony: 5507-5513), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa1066 - link to the publication
  13. How bioinformatics resources work with G4 RNAs
    Authors:
    J. Miskiewicz, J. Sarzynska, M. Szachniuk
    Academic press:
    Briefings in Bioinformatics (rok: 2021, tom: 22, strony: 45671), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bib/bbaa201 - link to the publication
  14. Entanglements of structure elements revealed in RNA 3D models
    Authors:
    M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2021, tom: 49, strony: 9625-9632), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab716 - link to the publication
  15. When will RNA get its AlphaFold moment?
    Authors:
    B. Schneider, B. Sweeney, A. Bateman, J. Cerny, T. Zok, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2023, tom: 51, strony: 9522-9532), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkad726 - link to the publication
  16. DrawTetrado to create layer diagrams of G4 structures
    Authors:
    M. Zurkowski, T. Zok, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 3835-3836), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac394 - link to the publication
  17. High-quality, customizable heuristics for RNA 3D structure alignment
    Authors:
    M. Zurkowski, M. Antczak, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: btad315), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad315 - link to the publication
  18. RNAspider: a webserver to analyze entanglements in RNA 3D structures
    Authors:
    K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: W663-W669), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac218 - link to the publication
  19. How bioinformatics resources work with G4 RNAs
    Authors:
    J. Miskiewicz, J. Sarzynska, M. Szachniuk
    Academic press:
    Briefings in Bioinformatics (rok: 2021, tom: 22, strony: 45671), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bib/bbaa201 - link to the publication
  20. WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures
    Authors:
    B. Adamczyk, M. Zurkowski, M. Szachniuk, T. Zok
    Academic press:
    Nucleic Acids Research (rok: 2023, tom: 51, strony: W607-W612), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkad346 - link to the publication
  21. RNAsolo: a repository of cleaned PDB-derived RNA 3D structures
    Authors:
    B.Adamczyk, M. Antczak, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 3668-3670), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac386 - link to the publication
  22. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
    Authors:
    F. Carrascoza, M. Antczak, Z. Miao, E. Westhof, M. Szachniuk
    Academic press:
    RNA (rok: 2022, tom: 28, strony: 250-262), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1261/rna.078685.121 - link to the publication
  23. Virxicon: a lexicon of viral sequences
    Authors:
    M. Kudla, K. Gutowska, J. Synak, M. Weber, K.S. Bohnsack, P. Lukasiak, T. Villmann, J. Blazewicz, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2020, tom: 36, strony: 5507-5513), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa1066 - link to the publication
  24. RNA tertiary structure prediction using RNAComposer in CASP15
    Authors:
    J. Sarzynska, M. Popenda, M. Antczak, M. Szachniuk
    Academic press:
    PROTEINS: Structure, Function, and Bioinformatics (rok: 2023, tom: 91, strony: 1790-1799), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.26578 - link to the publication
  25. BioCommons: a robust java library for RNA structural bioinformatics
    Authors:
    T. Zok
    Academic press:
    Bioinformatics (rok: 2021, tom: 37, strony: 2766-2767), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab069 - link to the publication
  26. In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients
    Authors:
    T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski
    Academic press:
    Applied Sciences (rok: 2020, tom: 10, strony: 7275), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/app10207275 - link to the publication
  27. BioCommons: a robust java library for RNA structural bioinformatics
    Authors:
    T. Zok
    Academic press:
    Bioinformatics (rok: 2021, tom: 37, strony: 2766-2767), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab069 - link to the publication
  28. DrawTetrado to create layer diagrams of G4 structures
    Authors:
    M. Zurkowski, T. Zok, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 3835-3836), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac394 - link to the publication
  29. RNAsolo: a repository of cleaned PDB-derived RNA 3D structures
    Authors:
    B.Adamczyk, M. Antczak, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 3668-3670), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac386 - link to the publication
  30. BioCommons: a robust java library for RNA structural bioinformatics
    Authors:
    T. Zok
    Academic press:
    Bioinformatics (rok: 2021, tom: 37, strony: 2766-2767), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab069 - link to the publication
  31. In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients
    Authors:
    T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski
    Academic press:
    Applied Sciences (rok: 2020, tom: 10, strony: 7275), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/app10207275 - link to the publication
  32. ONQUADRO: a database of experimentally determined quadruplex structures
    Authors:
    T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: D253-D258), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkab1118 - link to the publication

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