ProtienCNN‐BLSTM: An efficient deep neural network with amino acid embedding‐based model of protein sequence classification and biological analysis

Abstract

AbstractProtein sequence classification needs to be performed quickly and accurately to progress bioinformatics advancements and the production of pharmaceutical products. Extensive comparisons between large databases of known proteins and unknown sequences are necessary in traditional protein classification methods, which can be time‐consuming. This labour‐intensive and slow manual matching and classification method depends on functional and biological commonalities. Protein classification is one of the many fields in which deep learning has recently revolutionized. The data on proteins are organized hierarchically and sequentially, and the most advanced algorithms, such as Deep Family‐based Method (DeepFam) and Protein Convolutional Neural Network (ProtCNN), have shown promising results in classifying proteins into relative groups. On the other hand, these methods frequently refuse to acknowledge this fact. We propose a novel hybrid model called ProteinCNN‐BLSTM to overcome these particular challenges. To produce more accurate protein sequence classification, it combines the techniques of amino acid embedding with bidirectional long short‐term memory (BLSTM) and convolutional neural networks (CNNs). The CNN component is the most effective at capturing local features, while the BLSTM component is the most capable of modeling long‐term dependencies across protein sequences. Through the process of amino acid embedding, sequences of proteins are transformed into numeric vectors, which significantly improves the precision of prediction and the representation of features. Using the standard protein samples PDB‐14189 and PDB‐2272, we analyzed the proposed ProteinCNN‐BLSTM model and the existing deep‐learning models. Compared to the existing models, such as CNN, LSTM, GCNs, CNN‐LSTM, RNNs, GCN‐RNN, DeepFam, and ProtCNN, the proposed model performed more accurately and better than the existing models.