基于结构的单链和双链DNA结合蛋白的分类研究[EB/OL]
北京：中国科技论文在线
本文对HOLO和APO的非冗余单链DNA结合蛋白（SSBs）和双链DNA结合蛋白（DSBs）进行了分类研究
双链DNA结合蛋白 WANG Wei
提出一种蛋白质表面通道特征和OB结构域比对方法的分类模型
长度、曲率特征和基于蛋白结构域的结构比对方法
单链DNA结合蛋白
能够对蛋白的功能进行有效分类预测,并且本方法对DNA结合位点的预测、分子识别和药物设计等研究具有重要意义
） Abstract： Protein-DNA interactions are essential for many biological processes
However, the structural mechanisms underlying these interactions are not fully understood
We introduce a new motif called protein tunnel features and OB-fold structural alignment (OSA) to study the difference between double-stranded DNA-binding proteins (DSBs) and single-stranded DNA binding proteins (SSBs)
Based the incorporative features were constructed this classifiers with support vector machine (SVM)
The predictor was evaluated using a 10-fold cross validation in HOLO (36/218) and APO (36/46) non-redundant datasets
The best SVM classifier results achieved by our proposed method for: accuracy 83
23%, sensitivity 83
76%, specificity 79
75%, AUC 0
8842 and applied to the independent test; Moreover, HOLO and APO dataset were used to the independent test, and analyzed HOLO-APO proteins conformational change with DNA-binding
The results show that the properties of the surfaces bottleneck radius, tunnel length, and tunnel curvature conformational features can be applicable for de novo protein-function prediction
In conclusion, we present a novel methodology to characterize protein surface, which can accurately tell apart SSBs from DSBs
The strength of our method in recognizing fine-tuned differences on DNA binding interfaces make it applicable for many other molecular recognition problems, with potential implications for drug design
Keywords： protein structureal; single-stranded DNA-binding proteins (SSBs); double-stranded DNA-binding proteins (DSBs) 下载PDF阅读器 PDF全文下载： 初稿 （ 214 ） 作者简介： WANG Wei (1975), Male, PhD student, Bioinformatcis & Data mining 通信联系人： LIU Juan (1970), Female, Professor, Bioinformatcis & Data mining 【收录情况】 中国科技论文在线： 王伟
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