Abstract: Protein similarity comparison is an important way to study protein structure and function. Many methods are proposed which are capable of comparing all available protein structure. Being different from those methods, a new method based on multiple characters is provided. There are four characteristics and some internal relationships among the four characteristics. So a method based on fuzzy equivalent matrix is proposed in which the four characteristics are considered comprehensively.

Key words: computer application, similarity comparison, multiple characters framework, fuzzy equivalent matrixes