关键词: PSSM矩阵, BP神经网络, CB396数据集, 蛋白质二级结构

Abstract: In the traditional protein secondary prediction methods，it often be founded unbalance training，as a result of that there is a big difference among the three structures of the correct rate，which is caused by the different number of residues.In order to correct it，as to the bagging，rectifying the traditional method，reducing the difference of the number of residues.In experiment，the data of CB396 is used，get better correct rate of collapse and the three total rate get up to 77%，the method achieves better performance.

Key words: Position Special Scoring Matrix（PSSM）, BP neural network, CB396, protein secondary prediction