Prediction of viral-host interactions of COVID-19 by computational methods

• Published in: Chemometrics and intelligent laboratory systems 2022-09, Vol.228, p.104622-104622, Article 104622
• Main Authors: Alakus, Talha Burak, Turkoglu, Ibrahim
• Format: Article
• Language: English
• Subjects: Covid-19; Deep learning; Protein mapping; SARS-CoV-2 virus
• ISSN: 0169-7439; 1873-3239; 0169-7439
• DOI: 10.1016/j.chemolab.2022.104622

Experimental approaches are currently used to determine viral-host interactions, but these approaches are both time-consuming and costly. For these reasons, computational-based approaches are recommended. In this study, using computational-based approaches, viral-host interactions of SARS-CoV-2 virus and human proteins were predicted. The study consists of four different stages; in the first stage viral and host protein sequences were obtained. In the second stage, protein sequences were converted into numerical expressions by various protein mapping methods. These methods are entropy-based, AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters, EIIP, AESNN1, Miyazawa energies, Micheletti potentials, Z-scale, and hydrophobicity. In the third stage, a deep learning model was designed and BiLSTM was used for this. In the last stage, the protein sequences were classified, and the viral-host interactions were predicted. The performances of protein mapping methods were determined by accuracy, F1-score, specificity, sensitivity, and AUC scores. According to the classification results, the best classification process was obtained by the entropy-based method. With this method, 94.74% accuracy, and 0.95 AUC score were calculated. Then, the most successful classification process was performed with the Z-scale and 91.23% accuracy, and 0.96 AUC score were obtained. Although other protein mapping methods are not as efficient as Z-scale and entropy-based methods, they have achieved successful classification. AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters and AESNN1 methods showed over 80% accuracy, F1-score, and AUC score. Accuracy scores of EIIP, Miyazawa energies, Micheletti potentials and hydrophobicity methods remained below 80%. When the results were examined in general, it was observed that the computational approaches were successful in predicting viral-host interactions between SARS-CoV-2 virus and human proteins. •In this study, viral-host interactions between SARS-CoV-2 and human proteins were predicted by computational approaches.•FIBHASH, AVL-tree and entropy-based methods were applied to this field for the first time with this study.•In this study, viral-host interactions between SARS-CoV-2 and human proteins were effectively classified by deep learning.