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PEPOP specifications

Information


Unique identifier OMICS_08654
Name PEPOP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Registration required Yes
Maintained No

Maintainer


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Publications for PEPOP

PEPOP in publications

 (6)
PMCID: 5700104
PMID: 29167517
DOI: 10.1038/s41598-017-16176-w

[…] plasmid was constructed by cloning the pluxi protein e purchased from thermofisher into the clai-psti restriction sites of p14amp. repeated attempts were made to clone the protein e gene from the pepop1 plasmid (gifts from dr. jeff hasty), but the start codon for this gene was mutated in every colony sequenced (greater than ten colonies were sequenced). to minimise the potential mutation […]

PMCID: 5227168
PMID: 28127568
DOI: 10.1155/2016/6760830

[…] discotope dataset []. bepro and cep prediction is based on the detection of exposed residues ignoring the residues buried in the spatial structure, which may affect the reliability of predictions., pepop is structure-based method, which identifies clusters of accessible surface residues and segments that might form putative discontinuous epitopes and can be used to design immunogenic peptides. […]

PMCID: 4964399
PMID: 27376281
DOI: 10.3390/ijms17071023

[…] described in swisssidechain []. yongye et al. [] employed molecular dynamics simulation to investigate the cyclization of d-aa-containing peptides. yet another study [], devised an approach known as pepop that allows the prediction of the immunogenicity of peptides containing both l-aa and d-aa. lastly, in regards to the aforementioned point on computing molecular descriptors of d-aas, […]

PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] into two types, those using antibody information and those that do not. the vast majority of them do not use any antibody information (e.g. cep [], discotope [, ], ellipro [, ], pepito [], pepop [], seppa [, ], epitopia [] and others [, ]). consensus-based methods such as epces [] or the meta-server epsvr/epmeta [] are currently among the best-performing algorithms in this area []., […]

PMCID: 3736542
PMID: 23970944
DOI: 10.1155/2013/943636

[…] the available amino acid physicochemical properties and geometrical structure properties. in 2008, three conformational b-cell epitope prediction methods were proposed: ellipro [], pepito [], and pepop []. the main idea of ellipro attributes to the liner b-cell epitopes prediction method of thornton et al. []. ellipro predicts conformational b-cell epitopes by combining the geometric features […]


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PEPOP institution(s)
INRA, Unité de Biochimie et Physiologie Moléculaire des Plantes (B&PMP), IBIP, Montpellier, France; INSERM UMR-S 665, DSIMB, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; INTS, Paris, France; Laboratoire d’Excellence GR-Ex, Paris, France; Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Sys2Diag UMR 9005 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, Montpellier, France; Programa de PósGraduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, Santa Catarina, Brazil; Bio-Rad Laboratories, Montpellier, France; Department of Haematology, University Hospital, Nîmes, France; service d'hématologie biologique, CHU Clermont-Ferrand, France; CNRS, UMR5048, INSERM, U1054, Université Montpellier, Centre de Biochimie Structurale, Montpellier, France
PEPOP funding source(s)
Supported by grants from the Ministry of Research (France); University Paris Diderot, Sorbonne Paris Cité (France); the National Institute for Blood Transfusion (INTS, France); the brazilian instituitions CAPES, FAPEMIG and CNPQ; the Institute for Health and Medical Research (INSERM, France); and a Labex GR-Ex grant (France).

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