A 3-D presentation of protein secondary structure characteristic sequences

Similarity comparison of protein structure is an important problem in computational molecular biology. It plays an important role in predicting the structure and function of protein. This paper introduces a 3-D presentation of protein secondary structure based on eight-letter secondary structure alphabet and applies it to analyze the similarity among three different proteins (LYP, myoglobin101M and myoglobin102M). The result is satisfactory. This method does not rely on the one-dimensional amino acid sequences which we know well completely. But it relies on more conservative eight-letter sequences whose basic unit is protein secondary structure. It is an effective measure to analyze the similarity between two proteins with any structure. Especially, it has realistic significance to compare two proteins that have no sequence similarities.