It is well known that approximately 90% of B-cell epitopes (BCEs) are discontinuous in nature, which makes it difficult to mimic them for creating vaccines. To advance the performance of conformational B-cell epitope prediction in an antigen from its structure, several studies have proposed methods in the past that are listed below.

Name Year Description Pubmed ID
CEP 2005 CEP: a conformational epitope prediction server/Accessibility, Accessible Surface Area 15980448
DiscoTope 2006 Prediction of residues in discontinuous B-cell epitopes using protein 3D structures/Amino Acid Statistics, Spatial Information, And Surface Accessibility 17001032
ElliPro 2008 Structure-based tool for the prediction of antibody epitopes 19055730
PEPITO 2008 Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure/Propensity Scores And Half Sphere Exposure Values At Multiple Distances 18443018
SEPPA 2009 A computational server for spatial epitope prediction of protein antigens/Unit-patch of residue triangle and clustering coefficient 19465377
EPCES 2009 Prediction of B-Cell Antigenic Epitopes on Protein Surfaces with Conformational Information/Residue Epitope Propensity, Conservation Score, Side- Chain Energy Score, Contact Number, Surface Planarity Score, And Secondary Structure Composition 32162262
EPSVR 2010 Antigenic Epitopes Prediction with Support Vector Regression/Residue Epitope PropenSity, Conservation Score, Side Chain Energy Score, Contact Number Of The Central Residue, Surface Planarity Score, And Secondary Structure Composition 20637083
EPMeta 2010 A Meta Server for Prediction of Antigenic Epitopes/Meta Server 20637083
DiscoTope 2.0 2012 Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking/Sum Propensity Scores And Half-Sphere Exposure As A Surface Measure 23300419
SEPPA 2.0 2014 A server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen/Combines ASA (Accessible Surface Area) propensity of unit-triangle patches and amino acid index (AAindex) characteristics in the SEPPA algorithm 24838566
Seppa 3.0 2019 An enhanced spatial epitope prediction enabling glycoprotein antigens/Solvent Accessible Surface Areas (SASA) 36366745
CluSmote 2020 Enhancement of conformational B-cell epitope prediction using clusmote 33816926
SEMA SEMA 2022 Antigen B-cell conformational epitope prediction using deep transfer learning/Sema1D- Esm-1v Transformer, Protein Language Model Sema3D- Inverse Folding Models, Esm-If1 36189325
Epitope3D 2022 Machine learning method for conformational B-cell epitope prediction/Graph-Based Signatures 34676398