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

DOI10.1515/AMCS-2015-0050zbMATH Open1322.62182OpenAlexW2293818823WikidataQ57387698 ScholiaQ57387698MaRDI QIDQ747556FDOQ747556

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)

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

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• RNA secondary structure determination and representation based on constraints satisfaction

zbMATH Keywords

clusteringtorsion anglesconformer libraryneural gasRNA nucleotides

Mathematics Subject Classification ID

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

Cites Work

• Clustering by passing messages between data points
• Finding Groups in Data
• Least squares quantization in PCM
• Title not available (Why is that?)
• The Dissimilarity Representation for Pattern Recognition
• Modeling, inference and optimization of regulatory networks based on time series data
• MCQ4Structures to compute similarity of molecule structures
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• Center-based \(l_1\)-clustering method
• A statistical model of cluster stability
• Batch and median neural gas
• Some operations research methods for analyzing protein sequences and structures
• Regulation of p53 by SIRNA in radiation treated cells: simulation studies
• Divergence-based vector quantization

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

Uses Software

• apcluster
• APCluster
• MCQ4Structures
• RNA FRABASE
• clusfind

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