Background: Increasing numbers of researchers apply linear B-cell epitope prediction in
their research, as in the case of peptide-based vaccine design, diagnostic tests, disease prevention and
antibody production. Online software offers major ways of epitope prediction.
Objective: With the advent of more and more newly built software, a standard assessment for various
prediction tools is urgently needed.
Methods: From the users' perspective, we compared and evaluated the ability to correctly predict true
epitopes of six different B-cell epitope prediction softwares: Bepipred, ABCpred, AApred, LBtope,
BEST and SVMTrip, together with one Random group and five consensus groups. Fourteen experimentally
confirmed proteins (including 60 linear epitopes) were collected into an epitope database. Positive
value (PV) and minor predicted value (MPV) were used to quantify the method's prediction ability.
Results: Bepipred, AApred, BEST and LBtope performed significantly better than the Random group in
terms of PV and MPV. Based upon the average value of the two parameters, BEST was the most efficient
Conclusion: Bepipred, AApred and BEST are the most efficient tools for users to predict linear B-cell
epitopes. In addition, consensus groups have the effect of gathering true predicted results, but they fail
to greatly improve prediction performance.