Study on Relationship between Protein Sequence Pattern and Protein Secondary Structure

In this paper, the relation between protein sequence pattern and protein secondary structure is studied deeply. It first introduces the protein sequence pattern and organism-specific dictionary. Then four effect factors that may affect the secondary structure of protein sequence pattern are presented. One of the factors, protein sequence segment that matches the pattern is analyzed in detail. Amino acid effect on secondary structure and effect vector are defined for the first time. Finally, the secondary structure prediction method based on the effect vector is proposed. Experimental result shows that the effect of amino acid residues on secondary structure is both position-specific and structure-specific. Amino acid effect vector is important and effective in secondary structure prediction for patterns or proteins. The prediction accuracy rate can reach 80.2% for patterns with similar secondary structures