Building the library of RNA 3D nucleotide conformations using the clustering approach

DOI10.1515/AMCS-2015-0050MaRDI QIDQ747556zbMATH OpenOpenAlexWikidataFDO

Authors Tomasz Zok, Maciej Antczak, M. Riedel, David Nebel, Piotr Lukasiak, Jacek Blazewicz, Marta Szachniuk, Thomas Villmann

Publication date 16 October 2015

Published in International Journal of Applied Mathematics and Computer Science (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Full work available at URL https://doi.org/10.1515/amcs-2015-0050

zbMATH Keywords

clusteringtorsion anglesconformer libraryneural gasRNA nucleotides

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Genetics and epigenetics (92D10)

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Cites work

• scientific article; zbMATH DE number 3129892 (Why is no real title available?)
• scientific article; zbMATH DE number 3340881 (Why is no real title available?)
• A statistical model of cluster stability
• Batch and median neural gas
• Center-based \(l_1\)-clustering method
• Clustering by passing messages between data points
• Divergence-based vector quantization
• Finding Groups in Data
• Least squares quantization in PCM
• MCQ4Structures to compute similarity of molecule structures
• Modeling, inference and optimization of regulatory networks based on time series data
• Regulation of p53 by SIRNA in radiation treated cells: simulation studies
• Some operations research methods for analyzing protein sequences and structures
• The Dissimilarity Representation for Pattern Recognition

Cited in

(4)

• A NEW METHOD FOR RNA 3D STRUCTURAL COMPARISONS USING SIMULATED ANNEALING
• Tabu search for the RNA partial degradation problem
• New models and algorithms for RNA pseudoknot order assignment
• RNABC: Forward kinematics to reduce all-atom steric clashes in RNA backbone

Describes a project that uses

Uses Software

• clusfind
• RNA FRABASE
• MCQ4Structures
• APCluster
• apcluster

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