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In recent years, computational identification of immunogenic regions/segments in a given protein antigen has provided increasing assistance in guiding the experimental validation. Since the majority of the epitope area was dominated by discontinuous amino acids in the surface of protein antigens (Haste Andersen et al., 2006), a lot of efforts have been devoted into computing spatial/conformational epitopes based on protein structures. These methods can be roughly divided into two tracks, one of which proposing useful parameters to discriminate epitope residues from common surface ones, while the other focusing on various classification algorithm to improve the performance.
(Haste Andersen et al., 2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci.
(Qi et al., 2014) SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic Acids Res.