PredCSO: an ensemble method for the prediction of S-sulfenylation sites in proteins,Molecular Omics

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PredCSO: an ensemble method for the prediction of S-sulfenylation sites in proteins
Molecular Omics ( IF 3.0 ) Pub Date : 2018-06-14 , DOI: 10.1039/c8mo00089a
Lei Deng _{1,

2,

3} , Xiaojie Xu _{1,

2,

3} , Hui Liu _{1,

2,

3,

4,

5}

Affiliation

Protein S-sulfenylation is a type of reversible post-translational modification (PTM) through which cysteine (CYS) thiols of proteins are reversibly oxidized to cysteine sulfenic acids (CSO). Recent studies have shown that this event plays an essential role in cell signaling, transcriptional regulation and protein functions. Therefore, the identification of S-sulfenylation sites is important to understand the functions of S-sulfenylated proteins. In this study, we proposed PredCSO, a computational method for predicting S-sulfenylation sites in proteins. PredCSO is built on four kinds of features, including position-specific scoring matrix, position-specific amino acid propensity, the absolute solvent accessibility and four-body statistical pseudo-potential. In particular, 21 crucial features were refined out using a two-step feature selection procedure consisting of a max-relevance algorithm and a sequential backward elimination algorithm. To overcome the problem of imbalanced sample sizes, we adopt an ensemble method, which combines bootstrap resampling, gradient tree boosting and majority voting. Our performance evaluation shows that PredCSO achieves state-of-the-art performance in identifying S-sulfenylation sites in proteins.

中文翻译：

PredCSO：预测蛋白质中S-亚磺酰化位点的整体方法

蛋白质S-亚磺酰化是一种可逆的翻译后修饰（PTM），蛋白质的半胱氨酸（CYS）硫醇可通过其被可逆地氧化为半胱氨酸亚磺酸（CSO）。最近的研究表明，该事件在细胞信号传导，转录调控和蛋白质功能中起着至关重要的作用。因此，S-亚磺酰化位点的鉴定对于理解S-亚磺酰化蛋白的功能很重要。在这项研究中，我们提出了PredCSO，这是一种预测蛋白质中S-亚磺酰化位点的计算方法。PredCSO建立在四种特征上，包括位置特异性得分矩阵，位置特异性氨基酸倾向，绝对溶剂可及性和四体统计伪势。尤其是，使用两步特征选择程序（包括最大相关性算法和顺序后向消除算法）对21个关键特征进行了细化。为了克服样本量不平衡的问题，我们采用了集成方法，该方法将自举重采样，梯度树增强和多数表决相结合。我们的性能评估表明，PredCSO在鉴定蛋白质中的S-亚磺酰化位点方面达到了最先进的性能。

更新日期：2018-12-01

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