CarSitePred: an integrated algorithm for identifying carbonylated sites based on KNDUA-LNDOT resampling technique

Abstract

Carbonylated sites are the determining factors for functional changes or deletions in carbonylated proteins, so identifying carbonylated sites is essential for understanding the process of protein carbonylated and exploring the pathogenesis of related diseases. The current wet experimental methods for predicting carbonylated modification sites ae not only expensive and time-consuming, but also have limited protein processing capabilities and cannot meet the needs of researchers. The identification of carbonylated sites using computational methods not only improves the functional characterization of proteins, but also provides researchers with free tools for predicting carbonylated sites. Therefore, it is essential to establish a model using computational methods that can accurately predict protein carbonylated sites. In this study, a prediction model, CarSitePred, is proposed to identify carbonylation sites. In CarSitePred, specific location amino acid hydrophobic hydrophilic, one-to-one numerical conversion of amino acids, and AlexNet convolutional neural networks convert preprocessed carbonylated sequences into valid numerical features. The K-means Normal Distribution-based Undersampling Algorithm (KNDUA) and Localized Normal Distribution Oversampling Technology (LNDOT) were firstly proposed and employed to balance the K, P, R and T carbonylation training dataset. And for the first time, carbonylation modification sites were transformed into the form of images and directly inputted into AlexNet convolutional neural network to extract features for fitting SVM classifiers. The 10-fold cross-validation and independent testing results show that CarSitePred achieves better prediction performance than the best currently available prediction models. Availability: https://github.com/zuoyun123/CarSitePred.

Communicated by Ramaswamy H. Sarma

Keywords:

• The K-means Normal Distribution-based Undersampling Algorithm (KNDUA)
• Localized Normal Distribution Oversampling Technology (LNDOT)
• AlexNet convolutional neural network
• sequence analysis
• identifying carbonylated sites

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

https://github.com/zuoyun123/CarSitePred

Additional information

Funding

This work is supported by the National Natural Science Foundation of China [62302198]; Natural Science Foundation of Jiangsu Province of China [BK20231035]；National Key Research and Development Program of China [2021YFE010178]; National Natural Science Foundation of China [62176105]; Hong Kong Research Grants Council [PolyU 152006/19E].