Sequence-based prediction methods only rely on the primary sequence of an antigen without replying on the availability of the 3D structures for the prediction of the linear B-cell epitopes prediction. Previously developed methods predict conformational B-cell epitopes with reasonably high accuracy, but the limitation of these methods is that they require tertiary structure of the antigen. Experimental techniques like X-ray crystallography is used for determining the structure of a protein, is costly, tedious and time consuming. To overcome this limitation several methods has been proposed listed below.

Name Year Description Pubmed ID
Epitopia 2009 A web-server for predicting B-cell epitopes/Physico-chemical And Structural-Geometrical Features 19751513
CBTOPE 2010 Identification of conformational B-cell Epitopes in an antigen from its primary sequence/Binary Profile Of Pattern , Physiochemical Profile Of Patterns, Composition Profile Of Patterns 20961417
CBEP 2014 Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering/Evolutionary Profile, Secondary Structure, Disorder Zone, Dipeptide Composition, And Physicochemical Properties. 25045691
BepiPred-2.0 2017 Improving sequence-based B-cell epitope prediction using conformational epitopes/Computed Volume, Hydrophobicity, Polarity, Relative Surface Accessibility (RSA) and Secondary Structure (SS) 28472356
SEPIa 2017 Predicting conformational B-cell epitopes from the amino acid sequence/AAC, Hydrophilicity, Secondary Structure, Flexibility, Intrinsically Disordered Regions, Energy-Like, Solvent Accessibility, Solubility, Evolutionary Information 28183272