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

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 χ(2 )test, the probability density function of which can be accurately estimated.