Department of Structural Bioinformatics


 

Head:

Marta Szachniuk, PhD,

Associate Prof. IBCH PAS

 


Staff:

Mariusz Popenda, PhD;

Marcin Radom, PhD;

 


PhD Students:

Joanna Miśkiewicz, MSc;

Jakub Wiedemann, MSc;

Marcin Zabłocki, MSc Eng.


 

 

 

Rys. 1.


 

Rys. 2.


 

Rys. 3


 

Rys. 4


 

Rys. 5

 

 

Keywords:

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:

  • 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

 

Most important research achievements:

  • RNApolis, a webportal dedicated to RNA structural bioinformatics.
  • RNAComposer, the method for automated prediction of RNA 3D structure.
  • RNA FRABASE, a database system to store RNA structure data and search for structure motifs.
  • RNApdbee, a system to annotate and process knotted and unknotted RNA structures.
  • RNAfitme, the method to model and reconstruct full-atom RNA structures.
  • RNAvista, a webserver for automated prediction of extended RNA secondary structure.
  • MCQ, torsion-angle-based method to evaluate predicted 3D models of RNA.
  • LCS-TA, an algorithm for identification of similar fragments in RNA 3D structures.
  • Classification of tetrads and quadruplexes in nucleic acids structures.

 

Selected publications from the last three years:

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


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


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).


D. Formanowicz, M. Radom, A. Rybarczyk, P. Formanowicz, The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis; modeled and analyzed using a Petri net-based approach. Biosystems 165, 2018, 71-87. (doi:10.1016/j.biosystems.2018.01.002).


M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk, RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics, 2018, (doi:10.1093/bioinformatics/bty609).