Protein structural homology: a metric approach

The flexibility of the polypeptide fold of proteins is essentially due to the rotational freedom about the main chain bonds involving Cα atoms. The polypeptide fold can therefore be represented by virtual bonds joining consecutive Cα atoms. The ordered sequence of virtual torsion and bond angles involving these bonds can be used to specify the fold. Such representations can then be compared to reveal structural similarities using the Needleman & Wünsch algorithm, which has been developed for comparison of amino acid sequences. Such an approach is presented and illustrated with examples. The method is suitable for detecting structural similarities that extend over 7 or more residues