BCPREDS protocols

View BCPREDS computational protocol

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BCPREDS specifications

Information


Unique identifier OMICS_08223
Name BCPREDS
Interface Web user interface
Restrictions to use None
Input data Primary sequence (amino acid sequence in plain format)
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yasser El-Manzalawy <>

Publications for BCPREDS

BCPREDS in pipeline

2016
PMCID: 5267949
PMID: 28149040
DOI: 10.6026/97320630012082

[…] candidates, since naturally acquired antibodies generated against them inhibit erythrocyte invasion and in some cases result in the clinical protection from disease. we thus used in silico tools (bcpreds, netmhccons and netmhciipan 3.0) to predict b-cell epitopes (bces) and t-cell epitopes (tces) in two merozoite invasion proteins, eba175-rii and rh5. initially, we validated these tools using […]


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BCPREDS in publications

 (35)
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] methods (http://www.cbs.dtu.dk/services/bepipred/). furthermore, abcpred, based on learning methods of the machine, applies recurrent neural network (http://www.imtech.res.in/raghava/abcpred), and bcpreds, which are also based on the learning ability of the machine, applies to support vector machines (http://ailab.cs.iastate.edu/bcpreds/) and the immune epitope database and analysis resource […]

PMCID: 5875910
PMID: 29561952
DOI: 10.1590/1414-431X20186213

[…] both global (for the entire structure) and local (per residue) error estimates based on one single model. visualization of tertiary structure was performed using ucsf chimera 1.10.2 ()., abcpred (), bcpreds (), bcepred (), and bioinformatics predicted antigenic peptides (bpap) system () were used for predicting b cell epitopes of der f 33. abcpred predicted b cell epitopes in antigen sequences, […]

PMCID: 5808131
PMID: 29467739
DOI: 10.3389/fmicb.2018.00125

[…] 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 of pdb: 2c78 [elongation factor tu (ef-tu) complexed […]

PMCID: 5773588
PMID: 29348555
DOI: 10.1038/s41598-018-19456-1

[…] human host body,., b-cells are a key player of humoral immunity. an epitope corresponding to the b-cell receptor plays an important role in vaccine design following antibody production. therefore, bcpreds server was used to reliably predict the linear b-cell epitopes where bcpred was the selected prediction method. total 14 b-cell epitopes of 20mer length were predicted among the primary input […]

PMCID: 5763123
PMID: 29445754
DOI: 10.1155/2017/2680160

[…] capturing selected properties, such as those given by different propensity scales. relevant examples of b-cell epitope prediction methods based on ml include bepipred [], abcpred [], lbtope [], bcpreds [], and svmtrip []. datasets, training features, and algorithms used for developing these methods differ. bepipred is based on random forests trained on b-cell epitopes obtained […]


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BCPREDS institution(s)
Artificial Intelligence Laboratory, Iowa State University, Ames, IA, USA

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