Szachniuk Group (Formerly Adamiak)

Szachniuk group is from the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Adamiak is from the Institute of Bioorganic Chemistry, Polish Academy of Sciences.
(Click here to find more information about Szachniuk Group)

Publications:

  1. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res. 2020 Jan 24;48(2):576-588.
  2. Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW. Automated 3D structure composition for large RNAs. Nucleic Acids Res. 2012 Aug;40(14):e112.
  3. Sarzynska J, Popenda M, Antczak M, Szachniuk M. RNA tertiary structure prediction using RNAComposer in CASP15. Proteins. 2023 Dec;91(12):1790-1799.
  4. Antczak M, Popenda M, Zok T, Zurkowski M, Adamiak RW, Szachniuk M. New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinformatics. 2018 Apr 15;34(8):1304-1312.
  5. Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J. RNAlyzer–novel approach for quality analysis of RNA structural models. Nucleic Acids Res. 2013 Jul;41(12):5978-90.
  6. Szachniuk, M. RNApolis: Computational platform for RNA structure analysis. Found. Comput. Decision Sci. 44, 241–257 (2019).
  7. Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. RNAloops: a database of RNA multiloops. Bioinformatics. 2022 Sep 2;38(17):4200-4205. doi: 10.1093/bioinformatics/btac484. PMID: 35809063; PMCID: PMC9438955.
  8. Zok T, Kraszewska N, Miskiewicz J, Pielacinska P, Zurkowski M, Szachniuk M. ONQUADRO: a database of experimentally determined quadruplex structures. Nucleic Acids Res. 2022 Jan 7;50(D1):D253-D258.
  9. Antczak M, Popenda M, Zok T, Sarzynska J, Ratajczak T, Tomczyk K, Adamiak RW, Szachniuk M. New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure. Acta Biochim Pol. 2016;63(4):737-744.
  10. Popenda M, Zok T, Sarzynska J, Korpeta A, Adamiak RW, Antczak M, Szachniuk M. Entanglements of structure elements revealed in RNA 3D models. Nucleic Acids Res. 2021 Sep 27;49(17):9625-9632.
  11. Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. RNA. 2022 Feb;28(2):250-262.