The concept of compact structural domain (CSD) is proposed which means a maximal compactly - packing - fold composed of α helices and β sheets in secondary structure sequence. There are three kinds of CSDs, namely α domain, β domain and α/β domain. Then five classes of protein are defined. The mainly- α protein is constructed from one or several α domains, the mainly-β protein is constructed from one or several β domains, the α/β protein is constructed from one or several α/β domains, the multi-domain protein is constructed from two or more kinds of CSDs, and the ζ-class protein does not contain any CSD. A database of 1 261 globular proteins is classified into five classes. The classification is compared with SCOP's. The analysis of redundancy-deletion has been done. A prediction rule on structural class is given which is the generalization of previous work. The successful rate of the prediction is higher than 82%.
LI Xiao-Qin, LUO Liao-Fu. The Definition and Recognition of Protein Structural Class[J]. Progress in Biochemistry and Biophysics,2002,29(1):124-127
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