A local alignment method for protein structure motifs

A method for the comparison of protein three-dimensional substructures was developed. The method employs the double dynamic programming method of Taylor & Orengo but identifies multiple local alignments rather than a single global alignment. A modification based on the Smith Waterman algorithm for sequence alignment enables the automatic identification and growth of the most structurally similar local alignments irrespective of length and composition. The method can also be used in a search mode to match substructures. Roughly five minutes is required to find all Greek-key motifs in a protein of 100 residues. Two novel globin folds have been detected using the method, the antibiotic protein colicin A and diphtheria toxin, neither of which have any functional relationship to the globins.