pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module.

BACKGROUND: Lysine succinylation is a newly discovered protein post-translational modifications. Predicting succinylation sites helps investigate the metabolic disease treatments. However, the biological experimental approaches are costly and inefficient, it is necessary to develop efficient computational approaches. RESULTS: In this paper, we proposed a novel predictor based on ensemble dense blocks and an attention module, called as pSuc-EDBAM, which adopted one hot encoding to derive the feature maps of protein sequences, and generated the low-level feature maps through 1-D CNN. Afterward, the ensemble dense blocks were used to capture feature information at different levels in the process of feature learning. We also introduced an attention module to evaluate the importance degrees of different features. The experimental results show that Acc reaches 74.25%, and MCC reaches 0.2927 on the testing dataset, which suggest that the pSuc-EDBAM outperforms the existing predictors. CONCLUSIONS: The experimental results of ten-fold cross-validation on the training dataset and independent test on the testing dataset showed that pSuc-EDBAM outperforms the existing succinylation site predictors and can predict potential succinylation sites effectively. The pSuc-EDBAM is feasible and obtains the credible predictive results, which may also provide valuable references for other related research. To make the convenience of the experimental scientists, a user-friendly web server has been established ( http://bioinfo.wugenqiang.top/pSuc-EDBAM/ ), by which the desired results can be easily obtained.

iGly-IDN: Identifying Lysine Glycation Sites in Proteins Based on Improved DenseNet.

Lysine glycation is one of the most significant protein post-translational modifications, which changes the properties of the proteins and causes them to be dysfunctional. Accurately identifying glycation sites helps to understand the biological function and potential mechanism of glycation in disease treatments. Nonetheless, the experimental methods are ordinarily inefficient and costly, so effective computational methods need to be developed. In this study, we proposed the new model called iGly-IDN based on the improved densely connected convolutional networks (DenseNet). First, one hot encoding was adopted to obtain the original feature maps. Afterward, the improved DenseNet was adopted to capture feature information with the importance degrees during the feature learning. According to the experimental results, Acc reaches 66%, and Mathews correlation coefficient reaches 0.33 on the independent testing data set, which indicates that the iGly-IDN can provide more effective glycation site identification than the current predictors.

DeepDN_iGlu: prediction of lysine glutarylation sites based on attention residual learning method and DenseNet.

As a key issue in orchestrating various biological processes and functions, protein post-translational modification (PTM) occurs widely in the mechanism of protein's function of animals and plants. Glutarylation is a type of protein-translational modification that occurs at active ε-amino groups of specific lysine residues in proteins, which is associated with various human diseases, including diabetes, cancer, and glutaric aciduria type I. Therefore, the issue of prediction for glutarylation sites is particularly important. This study developed a brand-new deep learning-based prediction model for glutarylation sites named DeepDN_iGlu via adopting attention residual learning method and DenseNet. The focal loss function is utilized in this study in place of the traditional cross-entropy loss function to address the issue of a substantial imbalance in the number of positive and negative samples. It can be noted that DeepDN_iGlu based on the deep learning model offers a greater potential for the glutarylation site prediction after employing the straightforward one hot encoding method, with Sensitivity (Sn), Specificity (Sp), Accuracy (ACC), Mathews Correlation Coefficient (MCC), and Area Under Curve (AUC) of 89.29%, 61.97%, 65.15%, 0.33 and 0.80 accordingly on the independent test set. To the best of the authors' knowledge, this is the first time that DenseNet has been used for the prediction of glutarylation sites. DeepDN_iGlu has been deployed as a web server (https://bioinfo.wugenqiang.top/~smw/DeepDN_iGlu/) that is available to make glutarylation site prediction data more accessible.

iEnhancer-DCSV: Predicting enhancers and their strength based on DenseNet and improved convolutional block attention module.

Enhancers play a crucial role in controlling gene transcription and expression. Therefore, bioinformatics puts many emphases on predicting enhancers and their strength. It is vital to create quick and accurate calculating techniques because conventional biomedical tests take too long time and are too expensive. This paper proposed a new predictor called iEnhancer-DCSV built on a modified densely connected convolutional network (DenseNet) and an improved convolutional block attention module (CBAM). Coding was performed using one-hot and nucleotide chemical property (NCP). DenseNet was used to extract advanced features from raw coding. The channel attention and spatial attention modules were used to evaluate the significance of the advanced features and then input into a fully connected neural network to yield the prediction probabilities. Finally, ensemble learning was employed on the final categorization findings via voting. According to the experimental results on the test set, the first layer of enhancer recognition achieved an accuracy of 78.95%, and the Matthews correlation coefficient value was 0.5809. The second layer of enhancer strength prediction achieved an accuracy of 80.70%, and the Matthews correlation coefficient value was 0.6609. The iEnhancer-DCSV method can be found at https://github.com/leirufeng/iEnhancer-DCSV. It is easy to obtain the desired results without using the complex mathematical formulas involved.

pSuc-FFSEA: Predicting Lysine Succinylation Sites in Proteins Based on Feature Fusion and Stacking Ensemble Algorithm.

Being a new type of widespread protein post-translational modifications discovered in recent years, succinylation plays a key role in protein conformational regulation and cellular function regulation. Numerous studies have shown that succinylation modifications are closely associated with the development of many diseases. In order to gain insight into the mechanism of succinylation, it is vital to identify lysine succinylation sites. However, experimental identification of succinylation sites is time-consuming and laborious, and traditional identification tools are unable to meet the rapid growth of datasets. Therefore, to solve this problem, we developed a new predictor named pSuc-FFSEA, which can predict succinylation sites in protein sequences by feature fusion and stacking ensemble algorithm. Specifically, the sequence information and physicochemical properties were first extracted using EBGW, One-Hot, continuous bag-of-words, chaos game representation, and AAF_DWT. Following that, feature selection was performed, which applied LASSO to select the optimal subset of features for the classifier, and then, stacking ensemble classifier was designed using two-layer stacking ensemble, selecting three classifiers, SVM, broad learning system and LightGBM classifier, as the base classifiers of the first layer, using logistic regression classifier as the meta classifier of the second layer. In order to further improve the model prediction accuracy and reduce the computational effort, bayesian optimization algorithm and grid search algorithm were utilized to optimize the hyperparameters of the classifier. Finally, the results of rigorous 10-fold cross-validation indicated our predictor showed excellent robustness and performed better than the previous prediction tools, which achieved an average prediction accuracy of 0.7773 ± 0.0120. Besides, for the convenience of the most experimental scientists, a user-friendly and comprehensive web-server for pSuc-FFSEA has been established at https://bio.cangmang.xyz/pSuc-FFSEA, by which one can easily obtain the expected data and results without going through the complicated mathematics.