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Antioxidant Proteins' Identification Based on Support Vector Machine
Yuanke Xu1, Yaping Wen1, Guosheng Han1
1School of Mathematics and Computational Science, Xiangtan University, Hunan, China.
Background:
Evidence have increasingly indicated that for human disease, cell metabolism are deeply associated with proteins. Structural mutations and dysregulations of these proteins contribute to the development of the complex disease. Free radicals are unstable molecules that seek for electrons from the surrounding atoms for stability. Once a free radical binds to an atom in the body, a chain reaction occurs, which causes damage to cells and DNA. An antioxidant protein is a substance that protects cells from free radical damage. Accurate identification of antioxidant proteins is important for understanding their role in delaying aging and preventing and treating related diseases. Therefore, computational methods to identify antioxidant proteins have become an effective prior-pinpointing approach to experimental verification.
Methods:
In this study, support vector machines was used to identify antioxidant proteins, using amino acid compositions and 9-gap dipeptide compositions as feature extraction, and feature reduction by Principal Component Analysis.
Results:
The prediction accuracy Acc of this experiment reached 98.38%, the recall rate Sn of the positive sample was found to be 99.27%, the recall rate Sp of the negative sample reached 97.54%, and the MCC value was 0.9678. To evaluate our proposed method, the predictive performance of 20 antioxidant proteins from the National Center for Biotechnology Information(NCBI) was studied. As a result, 20 antioxidant proteins were correctly predicted by our method. Experimental results demonstrate that the performance of our method is better than the state-of-the-art methods for identification of antioxidant proteins.
Conclusion:
We collected experimental protein data from Uniport, including 253 antioxidant proteins and 1552 non-antioxidant proteins. The optimal feature extraction used in this paper is composed of amino acid composition and 9-gap dipeptide. The protein is identified by support vector machine, and the model evaluation index is obtained based on 5-fold cross-validation. Compared with the existing classification model, it is further explained that the SVM recognition model constructed in this paper is helpful for the recognition of antioxidized proteins.
Insights
This study introduces a computational method using support vector machines to accurately identify antioxidant proteins, crucial for understanding aging and disease. The developed model achieved high prediction accuracy, outperforming existing methods.
Area of Science:
- Biochemistry
- Computational Biology
- Proteomics
Background:
- Cell metabolism and protein dysregulation are linked to human diseases.
- Free radicals cause cellular and DNA damage.
- Antioxidant proteins protect against free radical damage, making their identification vital for health research.
Purpose of the Study:
- To develop and evaluate a computational method for identifying antioxidant proteins.
- To leverage machine learning for accurate and efficient prior-pinpointing of antioxidant proteins for experimental verification.
Main Methods:
- Utilized support vector machines (SVM) for protein identification.
- Employed amino acid composition and 9-gap dipeptide composition for feature extraction.
- Applied Principal Component Analysis (PCA) for feature reduction.
Main Results:
- Achieved a prediction accuracy of 98.38%, with a positive sample recall (Sn) of 99.27% and negative sample recall (Sp) of 97.54%.
- The model correctly predicted all 20 antioxidant proteins from the National Center for Biotechnology Information (NCBI) dataset.
- Demonstrated superior performance compared to state-of-the-art methods for antioxidant protein identification.
Conclusions:
- The developed SVM model, using amino acid and 9-gap dipeptide features, effectively identifies antioxidant proteins.
- The method shows significant utility for recognizing antioxidant proteins, aiding in disease research and therapeutic development.
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