Abstract
Antioxidant proteins play important roles in countering oxidative damage in organisms. Because it is time-consuming and has a high cost, the accurate identification of antioxidant proteins using biological experiments is a challenging task. For these reasons, we proposed a model using machine-learning algorithms that we named AOPs-SVM, which was developed based on sequence features and a support vector machine. Using a testing dataset, we conducted a jackknife cross-validation test with the proposed AOPs-SVM classifier and obtained 0.68 in sensitivity, 0.985 in specificity, 0.942 in average accuracy, 0.741 in MCC, and 0.832 in AUC. This outperformed existing classifiers. The experiment results demonstrate that the AOPs-SVM is an effective classifier and contributes to the research related to antioxidant proteins. A web server was built at http://server.malab.cn/AOPs-SVM/index.jsp to provide open access.
Highlights
The antioxidant system in organisms has the ability to prevent damage caused by reactive oxygen species (ROS) (Siswoyo et al, 2011)
Many extracted or purified proteins are used as natural antioxidants, including soy proteins, lactoferrin, casein, β-lactoglobulin, canola proteins, yam dioscorin, egg albumen proteins, maize zein, egg yolk phosvitin, and potato patatin
There are two groups of parameters that have to be determined in the proposed classifier: the parameters associated with the random forest in the feature selection phase, and the parameters associated with the optimizing SVM in the model generation phase
Summary
The antioxidant system in organisms has the ability to prevent damage caused by reactive oxygen species (ROS) (Siswoyo et al, 2011). Natural antioxidants are regarded as the second antioxidant defense line in organisms (Yigit et al, 2014), and have recently attracted increasing attention from researchers Such antioxidants are mainly extracted from dietary sources such as fruits, vegetables, and foods with carotenoids and vitamin A (Geetha et al, 2002; Podsedek, 2007; Tang et al, 2019a,b). When these antioxidants are consumed, they scavenge from the ROS and minimize the oxidative stress, reducing the risk to organisms (Yang et al, 2017). Proteins extracted from fertilized eggs, jellyfish, white beans, chickpeas, melinjo (gnetum gnemon) seeds, and ginkgo
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