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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


This tool is not available anymore.

Publications for PEPOP

PEPOP citations

 (8)
library_books

The spatiotemporal system dynamics of acquired resistance in an engineered microecology

2017
Sci Rep
PMCID: 5700104
PMID: 29167517
DOI: 10.1038/s41598-017-16176-w

[…] B15 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 of th […]

library_books

An Introduction to B Cell Epitope Mapping and In Silico Epitope Prediction

2016
J Immunol Res
PMCID: 5227168
PMID: 28127568
DOI: 10.1155/2016/6760830

[…] prediction tools is often difficult, especially when each of them has their own testing dataset. To solve this problem and help users to choose the tool, the recent web servers, CEP [], DiscoTope [], PEPOP [], ElliPro [], BEpro [], and SEPPA [], were tested with an independent dataset created by collection of the experimentally confirmed discontinuous epitopes. SEPPA gave the best performance amon […]

library_books

Roles of d Amino Acids on the Bioactivity of Host Defense Peptides

2016
Int J Mol Sci
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, a possible […]

library_books

Progress and challenges in predicting protein interfaces

2015
Brief Bioinform
PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] classified 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 []. […]

library_books

Bioinformatics Resources and Tools for Conformational B Cell Epitope Prediction

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

[…] nd half sphere exposure values at multiple distances. One major improvement of PEPITO is that it employed half sphere exposure to describe the degree of compactness which inspired the latter methods. PEPOP identifies segments composed of accessible and sequentially contiguous amino acids of the 3D structure of an antigen and then clusters these segments according to their spatial distances to iden […]

library_books

Vaccines: From Empirical Development to Rational Design

2012
PLoS Pathog
PMCID: 3493475
PMID: 23144616
DOI: 10.1371/journal.ppat.1003001

[…] use of learning machines that depend on quantitative data on known antibody epitopes led to the development of prediction tools for linear epitopes such as BCPREDS , and IMMUNOPRED , . In contrast, PEPOP , is based on 3-D structural data on antigen–antibody complexes, and it predicts discontinuous epitopes, their antigenicity, and immunogenicity, and suggests peptide constructs for synthesis. H […]

Citations

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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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