A Fast Method for Motif Detection and Searching in a Protein Structure Database

We present a data structure based on suffix trees that provides fast methods for searching three-dimensional polypeptide structures and for detecting common substructures (motifs) in a protein structure database. Unlike former approaches in this topic our approach does not consider the sequence of amino acids (i.e. the primary structure). Instead of that it uses a coding of the backbone torsion angles which is invariant to translation and rotation of the molecule in the actual coordinate system. By applying structural queries to a suffix tree that was build for the polypeptides in the Protein Data Bank (PDB) it is shown that the method works in practice and that it might be a very useful tool for future research in proteomics.     «

We present a data structure based on suffix trees that provides fast methods for searching three-dimensional polypeptide structures and for detecting common substructures (motifs) in a protein structure database. Unlike former approaches in this topic our approach does not consider the sequence of amino acids (i.e. the primary structure). Instead of that it uses a coding of the backbone torsion angles which is invariant to translation and rotation of the molecule in the actual coordinate system....     »