PSNO: predicting cysteine S-nitrosylation sites by incorporating various sequence-derived features into the general form of Chou's PseAAC

• Published in: International journal of molecular sciences Vol. 15; no. 7; pp. 11204 - 11219
• Main Authors: Zhang, Jian, Zhao, Xiaowei, Sun, Pingping, Ma, Zhiqiang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 25-06-2014; MDPI
• Subjects: Amino Acid Motifs; Amino acids; Biochemistry; Cysteine - metabolism; cysteine S-nitrosylation sites; incremental feature selection; k-nearest neighbor; Nitric Oxide - metabolism; Protein Processing, Post-Translational; relative entropy selection; Software
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms150711204

S-nitrosylation (SNO) is one of the most universal reversible post-translational modifications involved in many biological processes. Malfunction or dysregulation of SNO leads to a series of severe diseases, such as developmental abnormalities and various diseases. Therefore, the identification of SNO sites (SNOs) provides insights into disease progression and drug development. In this paper, a new bioinformatics tool, named PSNO, is proposed to identify SNOs from protein sequences. Firstly, we explore various promising sequence-derived discriminative features, including the evolutionary profile, the predicted secondary structure and the physicochemical properties. Secondly, rather than simply combining the features, which may bring about information redundancy and unwanted noise, we use the relative entropy selection and incremental feature selection approach to select the optimal feature subsets. Thirdly, we train our model by the technique of the k-nearest neighbor algorithm. Using both informative features and an elaborate feature selection scheme, our method, PSNO, achieves good prediction performance with a mean Mathews correlation coefficient (MCC) value of about 0.5119 on the training dataset using 10-fold cross-validation. These results indicate that PSNO can be used as a competitive predictor among the state-of-the-art SNOs prediction tools. A web-server, named PSNO, which implements the proposed method, is freely available at http://59.73.198.144:8088/PSNO/.