Selected Publications

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotatesmotifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/
Nucleic Acids Research, 2018

Comparison of molecular structures in order to identify their similarity is an important step in solving various problems derived from computational biology, like structure alignment and modelling, motif search or clustering. Thus, there is a constant need for the development of good measures to determine distances between the structures and tools to display these distances in an easily interpretable form. In the paper we present MCQ4Structures, a new method and tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss its unique features as compared with the other measures, including RMSD and LGA, and we show its experimental use in comparison of a number of 3D structures as well as evaluation of models predicted within RNA-Puzzles contest. MCQ4Structures software is available as a free Java WebStart application at: http://www.cs.put.poznan.pl/tzok/mcq/. The source code licensed under BSD can be downloaded from the same website.
Central European Journal of Operations Research, 2014

Recent Publications

More Publications

. RNApdbee 2.0: multifunctional tool for RNA structure annotation. Nucleic Acids Research, 2018.

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. New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinformatics, 2018.

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. LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinformatics, 2017.

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. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, 2017.

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. Running simultaneous Kepler sessions for the parallelization of parametric scans and optimization studies applied to complex workflows. Journal of Computational Science, 2017.

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. New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure. Acta Biochimica Polonica, 2017.

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. Distributed and cloud-based multi-model analytics experiments on large volumes of climate change data in the Earth System Grid Federation eco-system. 2016 IEEE International Conference on Big Data, 2016.

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. New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics, 2015.

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. Building the Library of RNA 3D Nucleotide Conformations Using the Clustering Approach. International Journal of Applied Mathematics and Computer Science, 2015.

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. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA, 2015.

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Recent & Upcoming Conferences

RNApdbee 2.0. 3D → 2D structure
2018-07-15 — 2018-07-27
RNApdbee 2.0: a multifunctional tool for RNA structure annotation (POSTER)
2018-07-01 — 2018-07-04
RNA Structure Annotation and Visualization with RNApdbee 2.0 (POSTER)
2018-06-28 — 2018-06-30
RNA Pseudoknot Analysis: A Graph-Coloring Approach
2018-06-14 — 2018-06-16
New functions in RNApdbee 2.0
2018-05-17 — 2018-05-18
New Approaches to Determine RNA Pseudoknot Order
2017-09-27 — 2017-09-29
New Approaches to Determine RNA Pseudoknot Order (POSTER)
2017-05-29 — 2017-06-04
Quality assessment of RNA 3D structures
2016-10-15 — 2016-10-16
Application of new functionalities of RNAComposer to improve prediction accuracy
2016-09-28 — 2016-09-30

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