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BepiPred specifications


Unique identifier OMICS_06994
Name BepiPred
Interface Web user interface
Restrictions to use None
Input data Some protein sequence(s).
Input format FASTA
Output data A page containing a navigation bar with various tabs. The ‘Summary’ tab shows each individual sequence result in a horizontal and vertical scrollable table, the ‘Log’ tab shows a log of the computations and possible errors that have occurred and the ‘Help’ tab contains tips and tricks and a detailed description of the output page.
Output format JSON, CSV
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Paolo Marcatili
  • person_outline Morten Nielsen

Additional information

Publications for BepiPred

BepiPred citations


Immune Informatic Analysis and Design of Peptide Vaccine From Multi epitopes Against Corynebacterium pseudotuberculosis

Bioinform Biol Insights
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337
call_split See protocol

[…] er GenBank NC_017730.1), as a component of the virulence factors of C pseudotuberculosis and presenting an immune profile previously reported, was used to map epitopes of immunodominant B cells using BepiPred software which is based on propensity scale methods ( Furthermore, ABCPred, based on learning methods of the machine, applies recurrent neural networ […]


Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] Antigenic regions in Aspergillus proteins were predicted using Kolaskar-Tongaonkar method implemented in EMBOSS package with a threshold of 1.0 and BepiPred 2.0 ( with the default threshold of 0.5. Note that only predicted antigenic regions with a length ≥6 amino acids were accounted in the later […]


Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross reactive antibodies and have adapted during evolution

Sci Rep
PMCID: 5862889
PMID: 29563531
DOI: 10.1038/s41598-018-23029-7

[…] Sequences of immunoreactive proteins were searched for potential epitopes using 15 predictive approaches: AAP, BCPred, BepiPred, CBTOPE, COBEpro, FBCPred, IgPred, SVMTrip, as well as BcePred based on seven amino acid physico-chemical scales, hydrophilicity, flexibility, accessibility, turns, antigenic propensity, expo […]


Proteome wide mapping of immune features onto Plasmodium protein three dimensional structures

Sci Rep
PMCID: 5847524
PMID: 29531293
DOI: 10.1038/s41598-018-22592-3

[…] tide antigen presented by B-cells on MHC class II molecules. To examine the location of predicted B-cell epitopes in relation to regions of known structure in P. falciparum we used the newly released BepiPred 2.0 (Figure ). Although a number of tools exist for predicting B-cell epitopes based on structural data,, we wished to assess the utility of a state-of-the-art method that only uses the linea […]


Antigenic and functional profiles of a Lawsonia intracellularis protein that shows a flagellin like trait and its immuno stimulatory assessment

PMCID: 5815190
PMID: 29448958
DOI: 10.1186/s13567-018-0515-0

[…] ce similarity analysis was assessed by creating multiple sequence alignments using CLUSTALW []. The antigenicity index (linear B-cell epitopes) for the LFliC protein was estimated in silico using the BepiPred 2.0 web server []. BepiPred 2.0 employs the hidden Markov model combined with amino acid propensity scales to predict epitope data derived from crystal structures by assessing surface accessi […]


Epitope Mapping of Streptococcus agalactiae Elongation Factor Tu Protein Recognized by Human Sera

Front Microbiol
PMCID: 5808131
PMID: 29467739
DOI: 10.3389/fmicb.2018.00125
call_split See protocol

[…] Additionally, we used web server for epitope localization prediction: Antibody Epitope Prediction applied methods—Emini Surface Accessibility Prediction (), Kolaskar & Tongaonkar Antigenicity () and Bepipred Linear Epitope Prediction (), as another cross method BCPREDS was used from B-cell epitope prediction server. For more detailed predictions, we used homology models made based on 3D structure […]

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BepiPred institution(s)
Department of Bio and Health Informatics, Technical University of Denmark, Kgs, Lyngby, Denmark; La Jolla, Institute for Allergy and Immunology, La Jolla, CA, USA; Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martın, Buenos Aires, Argentina
BepiPred funding source(s)
Supported by National Institutes of Health [HHSN272201200010C].

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