Effect Factors on Secondary Structure of Protein Sequence Pattern

Discovering the relationship between protein sequence pattern and protein secondary structure is important for accurately predicting secondary structure of protein sequence. A protein secondary structure pattern dictionary is constructed using protein sequence pattern and its corresponding secondary structure in this paper. Based on the constructed dictionary, we propose four effect factors on secondary structure of protein sequence pattern, including 1) the core pattern itself; 2) patterns or amino acid residues that neighbor with the core pattern; 3) patterns or amino acid residues that are far away from the core pattern; and 4) amino acid sequence segment that match the core pattern. Statistical measures are adopted to analyze these factors. The experimental result shows the reliability of these factors. The recognition of these effect factors presents new directions to predict protein secondary structure based on protein pattern dictionary.