Object
Title: Building the library of RNA 3D nucleotide conformations using the clustering approach
Creator:
Zok, Tomasz ; Antczak, Maciej ; Riedel, Martin ; Nebel, David ; Villmann, Thomas ; Lukasiak, Piotr ; Blazewicz, Jacek ; Szachniuk, Marta
Resource Type:
Contributor:
Byrski, Aleksander - ed. ; Kisiel-Dorohinicki, Marek - ed. ; Dobrowolski, Grzegorz - ed.
Subtitle:
Group publication title:
Abstract:
An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. ; Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i) backbone- and (ii) ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.
Publisher:
Zielona Góra: Uniwersytet Zielonogórski
Resource Identifier:
DOI:
Pages:
Source:
AMCS, volume 25, number 3 (2015) ; click here to follow the link
Language:
Rights:
Biblioteka Uniwersytetu Zielonogórskiego
Object collections:
- Repository > Faculties > Faculty of Computer, Electrical and Control Engineering
- Repository > Types of work > Articles
- Repository > Scientific journals and UZ publishing series > International Journal of Applied Mathematics and Computer Science (AMCS) > International Journal of Applied Mathematics and Computer Science (AMCS) (2015)
Last modified:
May 6, 2024
In our library since:
May 6, 2024
Number of object content hits:
51
All available object's versions:
https://zbc.uz.zgora.pl/repozytorium/publication/88911
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International Journal of Applied Mathematics and Computer Science (AMCS)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 26 (2016)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 25 (2015)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 25, number 1 (2015)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 25, number 2 (2015)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 25, number 3 (2015)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 26 (2016)
| Edition name | Date |
|---|---|
| Building the library of RNA 3D nucleotide conformations using the clustering approach | May 6, 2024 |
