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

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