Antioxidant proteins have been found closely linked to disease control for its ability to eliminate excess free radicals. Because of its medicinal value, the study of identifying antioxidant proteins is on the upsurge. Many machine-learning classifiers have performed poorly owing to the nonlinear and unbalanced nature of biological data. Recently, deep learning techniques showed advantages over many state-of-the-art machine learning methods in various fields. In this study, a deep learning based classifier was proposed to identify antioxidant proteins based on mixed g-gap dipeptide composition feature vector. The classifier employed deep autoencoder to extract nonlinear representation from raw input. The t-Distributed Stochastic Neighbor Embedding (t-SNE) was used for dimensionality reduction. Support vector machine was finally performed for classification. The classifier achieved F1 score of 0.8842 and MCC of 0.7409 in 10-fold cross validation. Experimental results show that our proposed method outperformed the traditional machine learning methods and could be a promising tool for antioxidant protein identification. For the convenience of others' scientific research, we have developed a user-friendly web server called IDAod for antioxidant protein identification, which can be accessed freely at http://bigroup.uestc.edu.cn/IDAod/.
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