Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison.
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.
Carugo
Oliviero
O
Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, Trieste, 34012, Italy. carugo@icgeb.trieste.it
Pongor
Sándor
S
D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D008958:Models, Molecular; D011336:Probability; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D017385:Sequence Homology; D012984:Software
D011506:Proteins