Zheng, WeiRuan, JishouHu, GangWang, KuiHanlon, MichelleGao, Jianzhao2015-11-182022-05-272022-05-272015Zheng W., Ruan J., Hu G., Wang K., Hanlon M., & Gao J. (2015). Analysis of conformational b-cell epitopes in the antibody-antigen complex using the depth function and the convex hull. PLoS ONE, 10(8), e0134835. doi:10.1371/journal.pone.0134835https://hdl.handle.net/20.500.14078/417The prediction of conformational b-cell epitopes plays an important role in immunoinformatics. Several computational methods are proposed on the basis of discrimination determined by the solvent-accessible surface between epitopes and non-epitopes, but the performance of existing methods is far from satisfying. In this paper, depth functions and the k-th surface convex hull are used to analyze epitopes and exposed non-epitopes. On each layer of the protein, we compute relative solvent accessibility and four different types of depth functions, i.e., Chakravarty depth, DPX, half-sphere exposure and half space depth, to analyze the location of epitopes on different layers of the proteins. We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr. Conformational bcell epitopes are rich in coils. Conservation of epitopes is not significantly lower than that of exposed non-epitopes. The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test. Epitopes are more likely to be located in the outer layer of the convex hull of a protein. On the benchmark dataset, the cumulate 10th convex hull covers 84.6% of exposed residues on the protein surface area, and nearly 95% of epitope sites. These findings may be helpful in building a predictor for epitopes.1.29 MBPDFenAttribution (CC BY)b cellsprotein structure predictioncrystal structureprotein structurearomatic amino acidsglycosylationstructural genomicsArticle