BepiPred specifications

Information


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

Maintainers


  • person_outline Paolo Marcatili <>
  • person_outline Morten Nielsen <>

Additional information


http://www.cbs.dtu.dk/services/BepiPred/instructions.php

Publications for BepiPred

BepiPred in publications

 (158)
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] 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 (http://www.cbs.dtu.dk/services/bepipred/). furthermore, abcpred, based on learning methods of the machine, applies recurrent neural […]

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

[…] immunotherapy, or used in vaccinations. to help prioritize aspergillus proteins, the abundance of antigenic regions (aar) value of proteins was calculated using two methods, kolaskar-tongaonkar and bepipred 2.0 (methods). the lower the aar value the more antigenic the protein. interestingly, in each aspergillus species, the average aar of the secretome is always significantly lower than cell […]

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

[…] protein families in the studied genomes were taken from orthomcl results., 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, […]

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

[…] within a given radius were calculated using the hopp-woods hydrophilicity scale and the kyte-doolittle hydrophobicity scale, respectively., potential b-cell epitopes were assessed using both bepipred 1.0 and bepipred 2.0, as we have previously used bepipred 1.0 when examining potential epitopes within disordered p. falciparum proteins but wished to utilise the more accurate bepipred 2.0 […]

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

[…] 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 […]


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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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