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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 in publications

 (8)
PMCID: 5778136
PMID: 29403456
DOI: 10.3389/fmicb.2018.00001

[…] 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 […]

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 […]

PMCID: 5227168
PMID: 28127568
DOI: 10.1155/2016/6760830

[…] log-odds ratios []. discotope has been recently updated to 2.0 version by kringelum and coworkers with several improvements for proper benchmark definitions and use and achieves an auc of 0.731 []., bepro server (formerly known as pepito) uses a combination of amino acid propensity scores along with side chain orientation and solvent accessibility information using half sphere exposure values […]

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

[…] carried out additional epitope predictions using the linear epitope prediction methods bayesb , cbtope , and cobepro , and the conformational epitope prediction methods ellipro , epsvr , seppa , and bepro ., t cell epitopes in pfceltos that bind to mhc class i and class ii epitopes for c57bl/6 and balb/c mice were predicted using the rankpep algorithm. in silico derived b and t cell epitopes […]

PMCID: 3669279
PMID: 23741517
DOI: 10.1371/journal.pone.0065855

[…] default settings, ), cobepro (continuous, default settings, ), cbtope (discontinuous, default settings, ), ellipro (discontinuous, default settings, ), discotope (discontinuous, default settings, ), bepro (discontinuous, default settings, select residues with score ≥0.5 ). a consensus epitope was defined as a region for which half of the methods predicted […]


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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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