DP-Bind: a Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
DP-Bind: a Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
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DOI：
10.1093/bioinformatics/btl672
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发表时间：
2007-03-01
期刊：
影响因子：
5.8
通讯作者：
Kuznetsov, Igor B.
中科院分区：
文献类型：
--
作者：
Hwang, Seungwoo;Gou, Zhenkun;Kuznetsov, Igor B.
这篇文章介绍了DP-Bind，一个用于从氨基酸序列预测DNA结合蛋白中DNA结合位点的Web服务器。Web服务器实现了三种机器学习方法：支持向量机，核逻辑回归和惩罚逻辑回归。可以单独使用输入序列或以PSI-BLAST位置特异性评分矩阵（PSSM）的形式自动生成的输入序列的进化保守性谱来进行预测。基于PSSM的核逻辑回归的准确性为77.2%，敏感性为76.4%，特异性为76.6%。所有三种单独方法的输出被组合成共识预测，以帮助识别具有高置信度的预测位置。可用性：可在http://lcg.rit.albany.edu/dp-bindContact免费获得：IKuznetsov@奥尔巴尼。eduSupplementry信息：http://lcg.rit.albany.edu/dp-bind/dpbind_supplement.html。
This article describes DP-Bind, a web server for predicting DNA-binding sites in a DNA-binding protein from its amino acid sequence. The web server implements three machine learning methods: support vector machine, kernel logistic regression and penalized logistic regression. Prediction can be performed using either the input sequence alone or an automatically generated profile of evolutionary conservation of the input sequence in the form of PSI-BLAST position-specific scoring matrix (PSSM). PSSM-based kernel logistic regression achieves the accuracy of 77.2%, sensitivity of 76.4% and specificity of 76.6%. The outputs of all three individual methods are combined into a consensus prediction to help identify positions predicted with high level of confidence.Availability: Freely available at http://lcg.rit.albany.edu/dp-bindContact: IKuznetsov@albany.eduSupplementry information: http://lcg.rit.albany.edu/dp-bind/dpbind_supplement.html.