Project Note

Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures

Svetlana Kirillova¹ and Oliviero Carugo^1,2

¹Department of Biomolecular Structural Chemistry, Programme of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria

²Department of General Chemistry, Pavia University, Viele Taramelli 12, I-27100 Pavia, Italy

author email corresponding author email

BMC Research Notes 2008, 1:44doi:10.1186/1756-0500-1-44

Published:	11 July 2008

Abstract

Background

Accurate and fast tools for comparing protein three-dimensional structures are necessary to scan and analyze large data sets.

Findings

The method described here is not only very fast but it is also reasonable precise, as it is shown by using the CATH database as a test set. Its rapidity depends on the fact that the protein structure is represented by vectors that monitors the distribution of the inter-residue distances within the protein core and the structure of which is optimized with the Freedman-Diaconis rule.

Conclusion

The similarity score is based on a χ² test, the probability density function of which can be accurately estimated.