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  • Title: Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison.
    Author: Carugo O, Pongor S.
    Journal: J Mol Biol; 2002 Jan 25; 315(4):887-98. PubMed ID: 11812155.
    Abstract:
    The distribution of the C(alpha)-C(alpha) distances between residues separated by three to 30 amino acid residues is highly characteristic of protein folds and makes it possible to identify them from a straightforward comparison of the distance histograms. The comparison is carried out by contingency table analysis and yields a probability of identity (PRIDE score), with values between zero and 1. For closely related structures, PRIDE is highly correlated with the root-mean-square distance between C(alpha) atoms, but it provides a correct classification even for unrelated structures for which a structural alignment is not meaningful. For example, an analysis of the CATH database of fold structures showed that 98.8% of the folds fall into the correct CATH homologous superfamily category, based on the highest PRIDE score obtained. Structural alignment and secondary-structure assignment are not necessary for the calculation of PRIDE, which is fast enough to allow the scanning of large databases.
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