Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

Table 2

Methods for structure-based B-cell epitopes prediction.

Method	Online service (program)	Brief notes (features used in prediction method)
CEP [30, 36]	Available upon request	First Web-based conformational B-cell epitopes prediction software, based on the surface accessible
DiscoTope [37]	http://www.cbs.dtu.dk/services/DiscoTope/	Amino acid statistics, spatial context, and surface accessibility
Rapberger^a [38]	Not stated	Based on antibody information
ElliPro [40]	http://tools.immuneepitope.org/tools/ElliPro/iedb_input	Prominent index
PEPITO/BEPro [41]	http://pepito.proteomics.ics.uci.edu/	Half sphere exposure values
PEPOP [42]	Available upon request	Accessible and sequence contiguous amino acids segments
SEPPA [45]	http://lifecenter.sgst.cn/seppa/index.php	Unit patch of residue triangle
Epitopia [46]	http://epitopia.tau.ac.il/	Based on Naïve Bayes classifier with physicochemical and structural geometrical properties
EPCES [47]	http://sysbio.unl.edu/services/EPCES/	Consensus score by six functions
Shinji Soga^a [49]	Not stated	Antibody-specific epitope propensity index
EPSVR & EPMeta [51]	http://sysbio.unl.edu/services/	Based on SVR and meta-analysis
Zhang^a [52]	http://code.google.com/p/my-project-bpredictor/downloads/list	Based on random forests with a; distance-based feature

aThe name of the first author is used if the method has no name.