title: An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks.
abstract: To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy.
authors.affiliation: The Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Lian
authors.affiliation: Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ze Chi
authors.initials: ZC
authors.lastname: Huang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Ge
authors.affiliation: The Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Xian Ming
authors.initials: XM
authors.lastname: Pan
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry / Q000276:immunology*; D012372:ROC Curve
chemical_list: D018985:Epitopes, B-Lymphocyte