title: PrAS: Prediction of amidation sites using multiple feature extraction.
abstract: Amidation plays an important role in a variety of pathological processes and serious diseases like neural dysfunction and hypertension. However, identification of protein amidation sites through traditional experimental methods is time consuming and expensive. In this paper, we proposed a novel predictor for Prediction of Amidation Sites (PrAS), which is the first software package for academic users. The method incorporated four representative feature types, which are position-based features, physicochemical and biochemical properties features, predicted structure-based features and evolutionary information features. A novel feature selection method, positive contribution feature selection was proposed to optimize features. PrAS achieved AUC of 0.96, accuracy of 92.1%, sensitivity of 81.2%, specificity of 94.9% and MCC of 0.76 on the independent test set. PrAS is freely available at https://sourceforge.net/p/praspkg.
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: tongwang1992@mail.nankai.edu.cn.
authors.forename: Tong
authors.initials: T
authors.lastname: Wang
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: jlspzw139@sina.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: wuyunqqg@163.com.
authors.forename: Qiqige
authors.initials: Q
authors.lastname: Wuyun
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: wu_zhenfeng@mail.nankai.edu.cn.
authors.forename: Zhenfeng
authors.initials: Z
authors.lastname: Wu
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. Electronic address: jsruan@nankai.edu.cn.
authors.forename: Jishou
authors.initials: J
authors.lastname: Ruan
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: huggs@nankai.edu.cn.
authors.forename: Gang
authors.initials: G
authors.lastname: Hu
authors.affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China. Electronic address: gaojz@nankai.edu.cn.
authors.forename: Jianzhao
authors.initials: J
authors.lastname: Gao
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D000595:Amino Acid Sequence; D019540:Area Under Curve; D019295:Computational Biology; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D060388:Support Vector Machine
chemical_list: D000577:Amides; D011506:Proteins
keywords: Amidation sites; Positive contribution feature selection; Posttranslational modification (PTM); Support vector machine (SVM)