SNP analysis combined with protein structure prediction defines structure-functional relationships in cancer related cytochrome P450 estrogen metabolism.

The P450 family of proteins has more than 1000 representatives, which despite sometimes relatively low sequence identity have a surprisingly high level of structural similarity. This fact makes this family of proteins ideal candidate for various types of modeling based on protein structure prediction. A number of P450 proteins, including CYPs 1A1, 1A2, 1B1, 3A4, 11B2, 17, and 19, play a role in the metabolism of estrogen.

Protein structural alignment for detection of maximally conserved regions.

An algorithm for comparison of homologous protein structures and for study of conformational changes in proteins, has been developed. The method is based on identification of pieces of the two molecules that have similar shapes, as determined by the local conformation of the polypeptide chain. Pieces that superpose within a specified tolerance are assembled into domains based on similar transformations for superposition.