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BEpro specifications

Information


Unique identifier OMICS_04196
Name BEpro
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for BEpro

BEpro citations

 (8)
library_books

Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017

2018
Front Microbiol
PMCID: 5778136
PMID: 29403456
DOI: 10.3389/fmicb.2018.00001

[…] acid substitutions were mapped on the predicted structure using Chimera v1.10.2 ().Next, we predicted B-cell conformational epitopes in the capsid protein in the structural models by DiscoTope2.0 (), BEPro (), EPCES (), and EPSVR (). We used these tools with cut-offs of -3.7 (DiscoTope2.0), 1.3 (BEPro), and 70 (EPCES, EPSVR). We accepted sites as B-cell conformational epitopes when they were infer […]

library_books

Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974–2015

2017
Front Microbiol
PMCID: 5723339
PMID: 29259596
DOI: 10.3389/fmicb.2017.02399

[…] 2006b: EF126965, Osaka 2007: AB434770, Apeldoorn 2007: GU270580, New Orleans 2009: GU445325, Sydney 2012: JX459908) were predicted using the following four tools: DiscoTope 2.0 (Kringelum et al., ), BEPro (Sweredoski and Baldi, ), EPCES (Liang et al., ), and EPSVR (Liang et al., ). Cut-off values of epitopes were set at −3.7 (DiscoTope 2.0), 1.3 (BEPro), and 70 (EPCES, EPSVR). Consensus sites in […]

library_books

An Introduction to B Cell Epitope Mapping and In Silico Epitope Prediction

2016
J Immunol Res
PMCID: 5227168
PMID: 28127568
DOI: 10.1155/2016/6760830

[…] inition of unit patch of residue triangle. Curated data of nonredundant spatial epitopes from PDB database was used for method testing. SEPPA outperforms popular prediction tools, CEP, DiscoTope, and BEpro, and achieves an average AUC over 0.742 [].Server ElliPro (derived from Ellipsoid and Protrusion) implements modified method for identifying continuous epitopes in the protein regions protruding […]

library_books

Computational and Experimental Validation of B and T Cell Epitopes of the In Vivo Immune Response to a Novel Malarial Antigen

2013
PLoS One
PMCID: 3745447
PMID: 23977087
DOI: 10.1371/journal.pone.0071610

[…] e prediction methods, CBTope performed the best with 58% and an AROC of 0.58 (p = 0.03), respectively, while in conformational epitope prediction, Ellipro achieved the highest accuracy with 66% while BEPro achieved the highest AROC of 0.73 (p<0.001). Overall the results of these newer methods did not show significant improvement over the older Bepipred, ABCpred, and Discotope methods in predicting […]

library_books

Evaluation and Use of In Silico Structure Based Epitope Prediction with Foot and Mouth Disease Virus

2013
PLoS One
PMCID: 3646828
PMID: 23667434
DOI: 10.1371/journal.pone.0061122

[…] with Epitopia performing significantly (P<0.05) better than both of these programs ( and ), in addition BEPro and Seppa also identified the least number of epitopes (), with Seppa identifying 34% and BEPro 22% of the total number respectively.All of the programs performed poorly in terms of precision (), with most results below 0.2. However all performed better in terms of accuracy of the results […]

library_books

Conformational B Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods

2013
PLoS One
PMCID: 3631208
PMID: 23620816
DOI: 10.1371/journal.pone.0062249

[…] computational complexity and the limited number of known antibody-antigen complex structures, only a limited number of prediction methods exist for discontinuous epitope prediction: CEP , DiscoTope , BEpro(PEPITO) , ElliPro , SEPPA , EPITOPIA , and EPCES , EPSVR , EPMeta , and Bpredictor . Since currently all discontinuous epitope prediction methods require the three-dimensional (3D) structures o […]

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BEpro institution(s)
Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA

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