Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method  

作　　者：Arash Rahmani Mokhtar Nosrati 

机构地区：[1]Department of Biotechnology,Faculty of Biological Science and Technology,University of Isfahan,Isfahan 0098-661573,Iran [2]Zistfile bioinformatics center,Sanandaj 0098-66158,Iran

出　　处：《Medical Data Mining》2023年第3期1-9,共9页TMR医学数据挖掘

摘　　要：Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

关 键 词：severe acute respiratory syndrome-like coronavirus machine learning Chou’s pseudo amino acid composition epitope based vaccine 

分 类 号：O62[理学—有机化学]