Acute-Phase-Specific Hepatapeptide Epitope for Diagnosis of Parvovirus B19 Infection

Kaikkonen, Leena; Lankinen, Hilkka; Harjunpää, Irene; Hokynar, Kati; Söderlund‐Venermo, Maria; Oker‐Blom, Christian; Hedman, Lea; Hedman, Klaus

doi:10.1128/jcm.38.2.944a-944a.2000

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“…As a result, we manually selected 11 proteins for which a total number of 65 BL epitope data were obtained. We selected the proteins from BciPep Database [22], HIV Molecular Immunology database (http://www.hiv.lanl.gov/content/immunology/index.html) and from the literature [23][24][25] (see database or author sources for each protein in Table 1). BciPep is a B epitope database focused on vaccine research projects and HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 T-cell epitopes and antibody binding sites.…”

Section: Proteins Studiedmentioning

confidence: 99%

Evaluation and Comparison of the Ability of Online Available Prediction Programs to Predict True Linear B-cell Epitopes

Costa¹,

Faccendini²,

Sferco³

et al. 2013

PPL

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This work deals with the use of predictors to identify useful B-cell linear epitopes to develop immunoassays. Experimental techniques to meet this goal are quite expensive and time consuming. Therefore, we tested 5 free, online prediction methods (AAPPred, ABCpred, BcePred, BepiPred and Antigenic) widely used for predicting linear epitopes, using the primary structure of the protein as the only input. We chose a set of 65 experimentally well documented epitopes obtained by the most reliable experimental techniques as our true positive set. To compare the quality of the predictor methods we used their positive predictive value (PPV), i.e. the proportion of the predicted epitopes that are true, experimentally confirmed epitopes, in relation to all the epitopes predicted. We conclude that AAPPred and ABCpred yield the best results as compared with the other programs and with a random prediction procedure. Our results also indicate that considering the consensual epitopes predicted by several programs does not improve the PPV.

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