PMID: 11604040Oct 18, 2001Paper

The influence of different structure representations on the clustering of an RNA nucleotides data set

Journal of Chemical Information and Computer Sciences
T H ReijmersL M Buydens

Abstract

The last couple of years an overwhelming amount of data has emerged in the field of biomolecular structure determination. To explore information hidden in these structure databases, clustering techniques can be used. The outcome of the clustering experiments largely depends, among others, on the way the data is represented; therefore, the choice how to represent the molecular structure information is extremely important. This article describes what the influence of the different representations on the clustering is and how it can be analyzed by means of a dendrogram comparison method. All experiments are performed using a data set consisting of RNA trinucleotides. Besides the most basic structure representation, the Cartesian coordinates representation, several other structure representations are used.

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jan 8, 1999·Journal of Molecular Biology·C M Duarte, A M Pyle

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Citations

Jan 15, 2013·Bioinformatics·Tim WiegelsAndrew E Torda
Jul 18, 2006·Nucleic Acids Research·Oranit DrorHaim J Wolfson
May 15, 2008·Nucleic Acids Research·Daniel SvozilBohdan Schneider
Oct 1, 2008·RNA·Mira AbrahamHaim J Wolfson
Jun 25, 2010·The Journal of Chemical Physics·Liang Liu, Shi-Jie Chen
Nov 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·Laura J W MurrayJane S Richardson
May 23, 2006·Current Opinion in Structural Biology·Neocles B LeontisEric Westhof
Jul 18, 2015·Nucleic Acids Research·Ping Ge, Shaojie Zhang

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