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Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl

Sekretariat Dyrektora, tel: 61 852 89 19

Address

Department of Structural Bioinformatics

Prof. Marta Szachniuk, associate professor

Head of Department
mszachniuk@ibch.poznan.pl
tel. 61 6653030

Researchers:

Dr. Marcin Radom

adiunkt

Dr. Mariusz Popenda

starszy specjalista chemik

Technical Staff:

Research Projects

  • models and algorithms for structure biology,
  • structure databases,
  • analysis of macromolecule structure parameters,
  • computational prediction of molecule structures,
  • 3D model comparison and similarity assessment

Research area

Keywords

  • Molecular structures and macromolecule interactions, with particular reference to RNA and RNA-protein interactions. 

  • Characterization of new bioinformatics issues related to study of biomolecule structures and their solution by means of new theoretical models definition and computational methods development. 

  • Performing in silico experiments, optionally supported by biological and chemical experiments. 

  • Development of the concept of virtual RNA bioinformatics laboratory and its implementation in RNApolis platform (http://rnapolis.pl/). 

  • Development of computational systems addressing current problems of structural biology, i.a., RNA FRABASE, RNAComposer, RNApdbee, RNAvista, RNAtango.

  • Modeling of RNA secondary and tertiary structure

  • Refinement of coarse-grained RNA 3D structure

  • Analysis of macromolecular structure in torsion angle space

  • Annotation and classification of pseudoknots

 

Research activity

Selected publications

  • 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, 2021 (doi:10.1080/07391102.2020.1844802).

  • J. Miskiewicz, J. Sarzynska, M. Szachniuk, How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics, 2021 (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).

  • M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao, RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research 48(2), 2020, 576-588 (doi: 10.1093/nar/gkz1108)

  • M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk, Topology-based classification of tetrads and quadruplex structures, Bioinformatics 36(4), 2020, 1129-1134 (doi:10.1093/bioinformatics/btz738)

  • T. Zok, M. Popenda, M. Szachniuk, ElTetrado: a tool for identification and classification of tetrads and quadruplexes, BMC Bioinformatics 21, 2020, 40 (doi:10.1186/s12859-020-3385-1)

  • Z. Miao, R.W. Adamiak, M. Antczak, M.J. Boniecki, J.M. Bujnicki, S-J. Chen, C.Y. Cheng, Y. Cheng, F-C. Chou, R. Das, N.V. Dokholyan, F. Ding, C. Geniesse, Y. Jiang, A. Joshi, A. Krokhotin, M. Magnus, O. Mailhot, F. Major, T.M. Mann, P. Piatkowski, R. Pluta, M. Popenda, J. Sarzynska, L. Sun, M. Szachniuk, S. Tian, J. Wang, A.M. Watkins, J. Wiedemann, X. Xu, J.D. Yesselman, D. Zhang, Z. Zhang, C. Zhao, P. Zhao, Y. Zhou, T. Zok, A. Zyla, A. Ren, R.T. Batey, B.L. Golden, L. Huang, D.M. Lilley, Y. Liu, D.J. Patel, E. Westhof, RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA 26, 2020, 982-995 (doi:10.1261/rna.075341.120)

  • M. Szachniuk, RNApolis: computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences 44(2), 2019, 241-257 (doi:10.2478/fcds-2019-0012).

  • M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk, RNAvista: a webserver to assess RNA secondary structures withnon-canonical base pairs, Bioinformatics 35(1), 2019, 152-155 (doi:10.1093/bioinformatics/bty609).

  • T. Zok, M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M. Szachniuk, RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research 46(W1), 2018, W30-W35 (doi:10.1093/nar/gky314).

  • M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk, RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics 19(1),2018, 304 (doi:10.1186/s12859-018-2317-9).

  • J. Miskiewicz, M. Szachniuk, Discovering structural motifs in miRNAprecursors from Viridiplantae kingdom, Molecules 23(6), 2018, 1367 (doi:10.3390/molecules23061367).

  • M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W. Adamiak, M. Szachniuk, New algorithms to represent complex pseudoknotted RNA structures indot-bracket notation, Bioinformatics 34(8), 2018, 1304-1312 (doi:10.1093/bioinformatics/btx783).