Analysis of conformational b-cell epitopes in the antibody-antigen complex using the depth function and the convex hull
dc.contributor.author | Zheng, Wei | |
dc.contributor.author | Ruan, Jishou | |
dc.contributor.author | Hu, Gang | |
dc.contributor.author | Wang, Kui | |
dc.contributor.author | Hanlon, Michelle | |
dc.contributor.author | Gao, Jianzhao | |
dc.date.accessioned | 2015-11-18 | |
dc.date.accessioned | 2022-05-27T01:14:30Z | |
dc.date.available | 2022-05-27T01:14:30Z | |
dc.date.issued | 2015 | |
dc.description.abstract | The 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. | |
dc.format.extent | 1.29 MB | |
dc.format.mimetype | ||
dc.identifier.citation | Zheng 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.0134835 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14078/417 | |
dc.language | English | |
dc.language.iso | en | |
dc.rights | Attribution (CC BY) | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.subject | b cells | |
dc.subject | protein structure prediction | |
dc.subject | crystal structure | |
dc.subject | protein structure | |
dc.subject | aromatic amino acids | |
dc.subject | glycosylation | |
dc.subject | structural genomics | |
dc.title | Analysis of conformational b-cell epitopes in the antibody-antigen complex using the depth function and the convex hull | en |
dc.type | Article | |
dspace.entity.type |
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