3-DIMENSIONAL STRUCTURAL FEATURE SEARCH OF PROTEINS

This paper describes a three-dimensional (3D) structural feature searc h, or motif search, of proteins using SS3D-P. Our present approach is based upon the use of a substructure searching program for small organ ic molecules, SS3D, reported in our previous work. In SS3D-P, the 3D s tructure of a protein is approximated with the coordinates of alpha-ca rbon atoms of the main chain, and treated as a molecular graph that is represented using a distance matrix. The program allows us to specify the tolerance value of the inter-residual distances to be compared. S everal characterization schemes are also available for the different a mino acid residues that can be distinguished. The program we have deve loped was validated by search trials with 3D query patterns of known p rotein motif structures: the P-loop, the EF-hand, and the Zinc finger motif using Protein Data Bank (PDB) structure files.