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Department of Structural Bioinformatics

prof. dr hab. inż. Marta Szachniuk

Prof. Marta Szachniuk
Head of Department

mszachniuk@cs.put.poznan.pl
Phone: ​​61 6653030

Technical Staff:

Dr. hab. Maciej Antczak, BEng.
starszy specjalista ​bioinformatyk

Dr. hab. ​Agnieszka Rybarczyk
starszy specjalista ​bioinformatyk

 Dr. Joanna Sarzyńska
senior researcher (biologist)

 Dr. Marcin Radom, BEng
starszy specjalista ​bioinformatyk

mgr inż. Bartosz Adamczyk
specjalista ​bioinformatyk

Research activity

Research area
  • Studying of molecular structures and macromolecule interactions, with particular reference to RNA and RNA-protein interactions.
  • Characterization of new bioinformatics issues related to structural biology of nucleic acids.
  • Design and execution of in silico experiments supported optionally by biological and chemical data.
  • Development of the RNApolis platform (http://rnapolis.pl/) - virtual RNA bioinformatics laboratory.
  • Development of computational systems addressing current problems of RNA biology, i.a., RNA FRABASE, RNAComposer, RNApdbee, RNAvista, RNAfitme, RNaspider.
  • Modeling of RNA secondary and tertiary structure.
  • Analysis of macromolecular structure in torsion angle space.
  • Annotation and classification of pseudoknots.
  • Development of computational systems for identification, analysis, and modeling of quadruplexes (as part of the SpaceTetrado bioinformatics toolkit).
Keywords
  • models ​and algorithms for structural biology,
  • structure databases,
  • web applications to analyze 2D and 3D structures of nucleic acids,
  • analysis of macromolecule structure parameters,
  • computational prediction of RNA structures,
  • 3D model comparison and similarity assessment,
  • automated identification and analysis of pseudoknots,
  • algorithms for classification and annotation of quadruplexes
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Research Projects

  • 2024/53/B/ST6/02789 ​Functional motif-targeted RNA structure modeling. NCN - OPUS 27 (MS)
  • 2020/39/O/ST6/01488 Predicting 3D RNA structures using Generative Adversarial Networks. NSC Poland - Preludium Bis 2 (MS)
  • 2019/35/B/ST6/03074 Feature exploration and modelling of quadruplex structures. NSC Poland - OPUS 18 (MS)
  • 2016/23/B/ST6/03931 RNApolis - methods and algorithms to model and analyze the RNA structure. NSC Poland - OPUS 12 (MS)

Selected publications

  • M. Weber, F. Erichson, M. Antczak, V. Schumann, J. Meitzner, T. Zok, F.D. Steffen, M. Szachniuk, R. Borner, FRET-guided selection of RNA 3D structures, Nucleic Acids Research 54(5), 2026, gkag147 (doi:10.1093/nar/gkag147). 
  • F. Bu, Y. Adam, R.W. Adamiak, M. Antczak, B.R.H. de Aquino, N.G. Badepally, R.T. Batey, E.F. Baulin, P. Boinski, M. J. Boniecki, J.M. Bujnicki, K.A. Carpenter, J. Chacon, S.J. Chen, W. Chiu, P. Cordero, N. K. Das, R. Das, W.K. Dawson, F. DiMaio, F. Ding, A.C. Dock-Bregeon, N. V. Dokholyan, R.O. Dror, S. Dunin-Horkawicz, S. Eismann, E. Ennifar, R. Esmaeeli, M.A. Farsani, A.R. Ferre-D'Amare, C. Geniesse, G.E. Ghanim, H. V. Guzman, I.V. Hood, L. Huang, D.S. Jain, F. Jaryani, L. Jin, A. Joshi, M. Karelina, J.S. Kieft, W. Kladwang, S. Kmiecik, D. Koirala, M. Kollmann, R.C. Kretsch, M. Kurcinski, J. Li, S. Li, M. Magnus, B. Masquida, S. N. Moafinejad, A. Mondal, S. Mukherjee, T.H.D. Nguyen, G. Nikolaev, C. Nithin, G. Nye, I.P.N. Pandaranadar Jeyeram, A. Perez, P. Pham, J.A. Piccirilli, S.P. Pilla, R. Pluta, S. Poblete, A. Ponce-Salvatierra, M. Popenda, L. Popenda, F. Pucci, R. Rangan, A. Ray, A. Ren, J. Sarzynska, C. M. Sha, F. Stefaniak, Z. Su, K.C. Suddala, M. Szachniuk, R. Townshend, R.J. Trachman III, J. Wang, W. Wang, A. Watkins, T.K. Wirecki, Y. Xiao, P. Xiong, Y. Xiong, J. Yang, J.D. Yesselman, J. Zhang, Y. Zhang, Z. Zhang, Y. Zhou, T. Zok, D. Zhang, S. Zhang, A. Zyla, E. Westhof, Z. Miao, RNA-Puzzles Round V: blind predictions of 23 RNA structures, Nature Methods 22, 2025, 399-411 (doi:10.1038/s41592-024-02543-9). 
  • M. Justyna, C.L. Zirbel, M. Antczak, M. Szachniuk, Graph Neural Network and Diffusion Model for modeling RNA interatomic interactions, Bioinformatics 41(9), 2025, btaf515 (doi:10.1093/bioinformatics/btaf515). 
  • J. Pielesiak, M. Antczak, M. Szachniuk, T. Zok, RNAtive to recognize native-like structure in a set of RNA 3D models, Bioinformatics 41(11), 2025, btaf601 (doi:10.1093/bioinformatics/btaf601). 
  • B.A. Gren, M. Antczak, T. Zok, J.I. Sulkowska, M. Szachniuk, Knotted artifacts in predicted 3D RNA structures, PLoS Computational Biology 20(6), 2024, e1011959 (doi:10.1371/journal.pcbi.1011959). 
  • M. Mackowiak, B. Adamczyk, M. Szachniuk, T. Zok, RNAtango: analysing and comparing RNA 3D structures via torsional angles, PLoS Computational Biology 20(10), 2024, e1012500 (doi:10.1371/journal.pcbi.1012500). 
  • B. Schneider, B. Sweeney, A. Bateman, J. Cerny, T. Zok, M. Szachniuk, When will RNA get its AlphaFold moment?, Nucleic Acids Research 51(18), 2023, 9522-9532 (doi:10.1093/nar/gkad726).
  • B. Adamczyk, M. Zurkowski, M. Szachniuk, T. Zok, WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures, Nucleic Acids Research 51(W1), 2023, W607-W612 (doi:10.1093/nar/gkad346).
  • M. Zurkowski, M. Antczak, M. Szachniuk, High-quality, customizable heuristics for RNA 3D structure alignment, Bioinformatics 39(5), 2023, btad315 (doi:10.1093/bioinformatics/btad315).
  • M. Justyna, M. Antczak, M. Szachniuk, Machine learning for RNA 2D structure prediction benchmarked on experimental data, Briefings in Bioinformatics 24(3), 2023, bbad153 (doi:110.1093/bib/bbad153).
  • J. Wiedemann, J. Kaczor, M. Milostan, T. Zok, J. Blazewicz, M. Szachniuk, M. Antczak, RNAloops: a database of RNA multiloops, Bioinformatics 38(17), 2022, 4200-4205 (doi:10.1093/bioinformatics/btac484).
  • T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk, ONQUADRO: a database of experimentally determined quadruplex structures, Nucleic Acids Research 50(D1), 2022, D253-D258 (doi:10.1093/nar/gkab1118).
  • F. Carrascoza, M. Antczak, Z. Miao, E. Westhof, M. Szachniuk, Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions, RNA 28(2), 2022, 250-262 (doi:10.1261/rna.078685.121).
  • K. Luwanski, V. Hlushchenko, M. Popenda, T. Zok, J. Sarzynska, D. Martsich, M. Szachniuk, M. Antczak, RNAspider: a webserver to analyze entanglements in RNA 3D structures, Nucleic Acids Research 50(W1), 2022, W663-W669 (doi:10.1093/nar/gkac218).
  • B. Adamczyk, M. Antczak, M. Szachniuk, RNAsolo: a repository of cleaned PDB-derived RNA 3D structures, Bioinformatics 38(14), 2022, 3668-3670 (doi:10.1093/bioinformatics/btac386).
  • A. Belter, M. Popenda, M. Sajek, T. Wozniak, M.Z. Naskret-Barciszewska, M. Szachniuk, S. Jurga, J. Barciszewski, A new molecular mechanism of RNA circularization and the microRNA sponge formation, Journal of Biomolecular Structure and Dynamics 40(7), 2022, 3038-3045 (doi:10.1080/07391102.2020.1844802).
  • M. Popenda, T. Zok, J. Sarzynska, A. Korpeta, R.W. Adamiak, M. Antczak, M. Szachniuk, Entanglements of structure elements revealed in RNA 3D models, Nucleic Acids Research 49(17), 2021, 9625-9632 (doi:10.1093/nar/gkab716).
  • J. Miskiewicz, J. Sarzynska, M. Szachniuk, How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics 22(3), 2021, bbaa201 (doi:10.1093/bib/bbaa201
  • T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski, In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, Applied Sciences 10(20), 2020, 7275 (doi:10.3390/app10207275).
  • J. Gumna, T. Zok, K. Figurski, K. Pachulska-Wieczorek, M. Szachniuk, RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, PLOS ONE 15(10), 2020, e0239287 (doi:10.1371/journal.pone.0239287).
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