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

BMC Research Notes
Svetlana Kirillova, Oliviero Carugo

Abstract

Accurate and fast tools for comparing protein three-dimensional structures are necessary to scan and analyze large data sets. 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. The similarity score is based on a chi2 test, the probability density function of which can be accurately estimated.

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Citations

Jul 31, 2013·Acta Crystallographica. Section D, Biological Crystallography·Oliviero Carugo, Kristina Djinovic-Carugo
May 20, 2009·BMC Bioinformatics·Alex StivalaPeter J Stuckey
Sep 4, 2010·BMC Bioinformatics·Alex D StivalaAnthony I Wirth
Mar 5, 2010·BMC Bioinformatics·Lei ZhangKotagiri Ramamohanarao

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Software Mentioned

FASTA
SHEBA
STRIDE
BLAST
VAST
PSI
IDEntity
PRIDE

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