Autor: Popenda, Mariusz - Katalog OPAC zbiorów

Skocz do pozycji: 1.

Tytuł:: Acid promoted transformations of fluorescent luminarosine and its 2-modified analogues
Autorzy:: Burdzy, Artur
Skalski, Bohdan
Paszyc, Stefan
Popenda, Mariusz
Adamiak, Ryszard
Powiązania:: https://bibliotekanauki.pl/articles/1044753.pdf
Data publikacji:: 1998
Wydawca:: Polskie Towarzystwo Biochemiczne
Źródło:: Acta Biochimica Polonica; 1998, 45, 4; 941-948
0001-527X
Pojawia się w:: Acta Biochimica Polonica
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 2.

Tytuł:: New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure
Autorzy:: Antczak, Maciej
Popenda, Mariusz
Zok, Tomasz
Sarzynska, Joanna
Ratajczak, Tomasz
Tomczyk, Katarzyna
Adamiak, Ryszard
Szachniuk, Marta
Powiązania:: https://bibliotekanauki.pl/articles/1038732.pdf
Data publikacji:: 2016
Wydawca:: Polskie Towarzystwo Biochemiczne
Tematy:: RNA 3D structure prediction
RNAComposer
plant miRNA precursor
Opis:: RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction, freely available at http://rnacomposer.cs.put.poznan.pl/ and http://rnacomposer.ibch.poznan.pl/. Its main components are: manually curated database of RNA 3D structure elements, highly efficient computational engine and user-friendly web application. In this paper, we demonstrate how the latest additions to the system allow the user to significantly affect the process of 3D model composition on several computational levels. Although in general our method is based on the knowledge of secondary structure topology, currently the RNAComposer offers a choice of six incorporated programs for secondary structure prediction. It also allows to apply a conditional search in the database of 3D structure elements and introduce user-provided elements into the final 3D model. This new functionality contributes to a significant improvement of the predicted 3D model reliability and it facilitates a better model adjustment to the experimental data. This is exemplified based on the RNAComposer application for modelling of the 3D structures of precursors of the miR160 family members.
Źródło:: Acta Biochimica Polonica; 2016, 63, 4; 737-744
0001-527X
Pojawia się w:: Acta Biochimica Polonica
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 3.

Tytuł:: New models and algorithms for RNA pseudoknot order assignment
Autorzy:: Zok, Tomasz
Badura, Jan
Swat, Sylwester
Figurski, Kacper
Popenda, Mariusz
Antczak, Maciej
Powiązania:: https://bibliotekanauki.pl/articles/911230.pdf
Data publikacji:: 2020
Wydawca:: Uniwersytet Zielonogórski. Oficyna Wydawnicza
Tematy:: RNA pseudoknot order
conflict graph
vertex coloring
maximum independent set
integer programming
kolorowanie grafu
zbiór niezależny
programowanie całkowitoliczbowe
Opis:: The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the pseudoknot order: a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.
Źródło:: International Journal of Applied Mathematics and Computer Science; 2020, 30, 2; 315-324
1641-876X
2083-8492
Pojawia się w:: International Journal of Applied Mathematics and Computer Science
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 4.

Tytuł:: Z-RNA. The synthesis of 2-O-[^13C]methyl- and 5-methyl-analogs of ribo-CGCGCG
Autorzy:: Biała, Ewa
Milecki, Jan
Kowalewski, Andrzej
Popenda, Mariusz
Antkowiak, Wiesław
Adamiak, Ryszard
Powiązania:: https://bibliotekanauki.pl/articles/1045444.pdf
Data publikacji:: 1993
Wydawca:: Polskie Towarzystwo Biochemiczne
Źródło:: Acta Biochimica Polonica; 1993, 40, 4; 521-530
0001-527X
Pojawia się w:: Acta Biochimica Polonica
Dostawca treści:: Biblioteka Nauki

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