Beyond Bioinformatics

Title

Clustering tendency in the protein fold space

Authors

Oliviero Carugo

Affiliation

Department of General Chemistry, Pavia University, viale Taramelli 12, I-27100 Pavia, Italy and Department of Biomolecular Structural Chemistry, MFPL - Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria

Email

oliviero.carugo@univie.ac.at

Article Type

Hypothesis

Date

Received June 20, 2009; Accepted July 23, 2009; Published February 28, 2010

Abstract

Several non-redundant ensembles of protein three-dimensional structures were analyzed in order to estimate their natural clustering tendency by means of the Cox-Lewis coefficient. It was observed that, despite proteins tend to aggregate into different and well separated groups, some overlap between different clusters occurs. This suggests that classifications bases only on structural data cannot allow a systematic classification of proteins. Additional information are in particular needed in order to monitor completely the complex evolutionary relationships between proteins.

Keywords

Cluster analysis; Clustering tendency; Protein fold; Protein structural domains; Protein structure classification.

Citation

Carugo, Bioinformation 4(8): 347-351 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.