Predicting C- and S-linked Glycosylation sites from protein sequences using protein language models

Among various post-translational modifications (PTMs), predicting C-linked and S-linked glycosites is an essential task, yet experimental techniques such as Capillary Electrophoresis (CE), Enzymatic Deglycosylation, and Mass Spectrometry (MS) are expensive. Therefore, computational techniques are required to predict these glycosites. Here, different language model embeddings and sequential features were explored. Two separate feature selection methods: Recursive Feature Elimination (RFE) and Particle Swarm Optimization (PSO) were employed and utilized for identifying the optimal feature set. Cross-validation results were generated for choosing the final models. Three sampling strategies to handle imbalanced datasets were examined: Random undersampling, Synthetic Minority Over-sampling Technique (SMOTE) and Adaptive Synthetic Sampling Approach for Imbalanced Learning (ADASYN).

In this study, two models: DeepCSEmbed-C and DeepCSEmbed-S are proposed for C-linked and S-linked glycosylation prediction respectively. DeepCSEmbed-C is a dual-branch deep learning model comprising a Feedforward Neural Network (FNN) branch and an Inception branch, coupled with a Random undersampling strategy. DeepCSEmbed-S is a Categorical Boosting (CAT) model with the SMOTE oversampling strategy. DeepCSEmbed-C outperformed available state-of-the-art (SOTA) methods, achieving 92.9% sensitivity, 95.1% F1-score and 90.6% MCC on the Independent dataset. Datasets and python scripts for training and testing the models are provided and made freely accessible at https://github.com/nafcoder/DeepCSEmbed.