一种预测判断蛋白质DNA相互作用位点的新方法  

A new method to predict Protein-DNA binding sites

作　　者：王皆恒 李校[1] WANG Jie-Heng;LI Xiao(Sichuan Key Laboratory of Molecular Biology and Biotechnology,College of Life Sciences,Sichuan University,Chengdu 610064,China)

机构地区：[1]四川大学生命科学学院四川省分子生物与生物技术重点实验室,成都610064

出　　处：《四川大学学报（自然科学版）》2020年第5期1009-1014,共6页Journal of Sichuan University(Natural Science Edition)

基　　金：国家自然科学基金(61001149)。

摘　　要：蛋白质-DNA相互作用位点在各类生理生化反应中扮演重要角色.本论文旨在构建一种可以准确预测"相互作用位点"的方法:PdDNA,其内容主要包括支持向量机和序列匹配器.支持向量机通过提取相互作用位点中心残基的特征进行训练并分类,序列匹配器则通过蛋白质特征矩阵(PSSM)对氨基酸序列进行相关性评估,对二者结果进行归一化整合,得到最终的预测结果.利用公开数据集PDNA62,我们的PdDNA预测准确率为86.87%.为进一步验证PdDNA可靠性,我们还自建了PDNA224数据集,其预测准确率为83.07%,处于较高水平.因此PdDNA是一种有效的"蛋白质-DNA相互作用位点"预测方法.Protein-DNA binding sites play an important role in various physiological and biochemical reactions.In this paper,we establish a special method and algorithm based on Bioinformatics to forecast Protein-DNA binding sites,we call it PdDNA.According to our method we have 2 mainly algorithm:SVM-based predictor and sequence-based predictor.SVM-based predictor is trained and classified by extracting features of central residues at binding sites,and sequence-based predictor scores amino acid sequences for correlation by Position-Specific Scoring Matrix(PSSM).Normalization and integration of the two results to obtain the final forecast.According to our algorithm,it predicts DNA-binding sites with 86.87%accuracy when tested on PDNA62 dataset.Otherwise,we established PDNA224 data set,and PdDNA also has 83.07%accuracy at a high level.Therefore,PdDNA is an effective method for predicting"Protein-DNA binding sites".

关 键 词：蛋白质-DNA相互作用位点预测 支持向量机 序列匹配算法 

分 类 号：Q811.4[生物学—生物工程]