Identification of B-cell epitopes(BCEs)plays an essential role in the development of pep-tide vaccines and immuno-diagnostic reagents,as well as antibody design and production.In this work,we generated a large benchmark dataset comprising 124,879 experimentally supported linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell assays.Analysis of this curated dataset showed large pathogen diversity covering 176 different families.The accuracy in linear BCE prediction was found to strongly vary with different features,while all sequence-derived and structural features were informative.To search more efficient and interpretive feature representations,a ten-layer deep learning framework for linear BCE prediction,namely NetBCE,was developed.NetBCE achieved high accuracy and robust performance with the average area under the curve(AUC)value of 0.8455 in five-fold cross-validation through automatically learning the informative classification features.NetBCE substantially outperformed the conventional ma-chine learning algorithms and other tools,with more than 22.06％improvement of AUC value com-pared to other tools using an independent dataset.Through investigating the output of important network modules in NetBCE,epitopes and non-epitopes tended to be presented in distinct regions with efficient feature representation along the network layer hierarchy.The NetBCE is freely avail-able at .

Haodong Xu;Zhongming Zhao

Center for Precision Health,School of Biomedical Informatics,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA;Human Genetics Center,School of Public Health,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA;The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences,Houston,TX 77030,USA;Department of Biomedical Informatics,Vanderbilt University Medical Center,Nashville,TN 37203,USA

基因组蛋白质组与生物信息学报（英文版）

[1]Haodong Xu;Zhongming Zhao-.NetBCE:An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes)[J].基因组蛋白质组与生物信息学报（英文版）,2022(05):1002-1012

NetBCE,Epitopes

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