Research On Sequence Similarity Search Using Fractal Features Of Proteins

Establishment of similarities between proteins is very important for the study of the relationship between sequence, structure and function and for the analysis of evolutionary relationships.A new method for finding similarity in 3-D protein structure comparison is proposed and tested. This method is grounded in the theory of fractal geometry. It is found that the structures of proteins are of self-similarity, such a phenomenon can be well described by their fractal dimensions. Fractal geometry has proven to be a useful tool in quantifying the structure of a wide range of idealized and naturally occurring objects, from pure mathematics, through physics and chemistry, to biology and medicine.The size and the volume fractal dimensionality of proteins to characterize the spatial complexity of the protein shape. Such quantitative measurement is helpful to reduce the search space when we retrieve protein structures from large data sets. The fractal features of a set of 74 protein structures selected from PDB (Protein Data Bank) was calculated. The experimental results show that the method is very effective in classification of 3-D protein structures and is helpful to reduce the search space when protein structures are retrieved from large data sets.