Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins

A novel algorithm has been developed for scoring the match between an imprecise sparse signature and all the protein sequences in a sequence database. The method was applied to a specific problem: signatures were derived from the probable folding nucleus and positions obtained from the determined interactions that occur during the folding of three small globular proteins and points of inter-element contact and sequence comparison of the actual three-dimensional structures of the same three proteins. In the case of two of these, lysozyme and myoglobin, the residues in the folding nucleus corresponded well to the key residues spotted by examination of the structures and in the remaining case, barnase, they did not. The diagnostic performance of the two types of signatures were compared for all three proteins. The significance of this for the application of an understanding of the protein folding mechanisms for structure prediction is discussed. The algorithm is generic and could be applied to other user-defined problems of sequence analysis.