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DPROT:利用进化信息预测无序蛋白质。

DPROT: prediction of disordered proteins using evolutionary information.

作者信息

Sethi Deepti, Garg Aarti, Raghava G P S

机构信息

Scientist and Head Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh, India.

出版信息

Amino Acids. 2008 Oct;35(3):599-605. doi: 10.1007/s00726-008-0085-y. Epub 2008 Apr 19.

Abstract

The association of structurally disordered proteins with a number of diseases has engendered enormous interest and therefore demands a prediction method that would facilitate their expeditious study at molecular level. The present study describes the development of a computational method for predicting disordered proteins using sequence and profile compositions as input features for the training of SVM models. First, we developed the amino acid and dipeptide compositions based SVM modules which yielded sensitivities of 75.6 and 73.2% along with Matthew's Correlation Coefficient (MCC) values of 0.75 and 0.60, respectively. In addition, the use of predicted secondary structure content (coil, sheet and helices) in the form of composition values attained a sensitivity of 76.8% and MCC value of 0.77. Finally, the training of SVM models using evolutionary information hidden in the multiple sequence alignment profile improved the prediction performance by achieving a sensitivity value of 78% and MCC of 0.78. Furthermore, when evaluated on an independent dataset of partially disordered proteins, the same SVM module provided a correct prediction rate of 86.6%. Based on the above study, a web server ("DPROT") was developed for the prediction of disordered proteins, which is available at http://www.imtech.res.in/raghava/dprot/.

摘要

结构紊乱蛋白质与多种疾病的关联引发了极大的兴趣,因此需要一种预测方法,以便在分子水平上促进对它们的快速研究。本研究描述了一种计算方法的开发,该方法使用序列和轮廓组成作为支持向量机(SVM)模型训练的输入特征来预测紊乱蛋白质。首先,我们开发了基于氨基酸和二肽组成的SVM模块,其灵敏度分别为75.6%和73.2%,马修斯相关系数(MCC)值分别为0.75和0.60。此外,以组成值的形式使用预测的二级结构含量(卷曲、片层和螺旋),灵敏度达到76.8%,MCC值为0.77。最后,使用隐藏在多序列比对轮廓中的进化信息训练SVM模型,通过达到78%的灵敏度值和0.78的MCC值提高了预测性能。此外,当在部分紊乱蛋白质的独立数据集上进行评估时,相同的SVM模块提供了86.6%的正确预测率。基于上述研究,开发了一个用于预测紊乱蛋白质的网络服务器(“DPROT”),可在http://www.imtech.res.in/raghava/dprot/上获取。

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