ORS-Pred: An optimized reduced scheme-based identifier for antioxidant proteins.

Changli Feng, Haiyan Wei, Deyun Yang, Bin Feng, Zhaogui Ma, Shuguang Han, Quan Zou, Hua Shi

Proteomics 2021 Aug

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Antioxidant proteins can terminate a chain of reactions caused by free radicals and protect cells from damage. To identify antioxidant proteins rapidly, a computational model was proposed based on the optimized recoding scheme, sequence information and machine learning methods. First, over 600 recoding schemes were collected to build a scheme set. Then, the original sequence was recoded as a reduced expression whose g-gap dipeptides (g = 0, 1, 2) were used as the features of proteins. Furthermore, a random forest method was used to evaluate the classification ability of the obtained dipeptide features. After going through all schemes, the best predictive performance scheme was chosen as the optimized reduction scheme. Finally, for the RF method, a grid search strategy was used to select a better parameter combination to identify antioxidant proteins. In the experiment, the present method correctly recognized 90.13-99.87% of the antioxidant samples. Other experimental results also proved that the present method was efficient to identify antioxidant proteins. Finally, we also developed a web server that was freely accessible to researchers. © 2021 Wiley-VCH GmbH.

Citation

Changli Feng, Haiyan Wei, Deyun Yang, Bin Feng, Zhaogui Ma, Shuguang Han, Quan Zou, Hua Shi. ORS-Pred: An optimized reduced scheme-based identifier for antioxidant proteins. Proteomics. 2021 Aug;21(15):e2100017