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NetCTLpan specifications

Information


Unique identifier OMICS_06756
Name NetCTLpan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Morten Nielsen

Publication for NetCTLpan

NetCTLpan citations

 (14)
library_books

Flagellin fused protein targeting M2e and HA2 induces potent humoral and T cell responses and protects mice against various influenza viruses a subtypes

2018
J Biomed Sci
PMCID: 5891888
PMID: 29631629
DOI: 10.1186/s12929-018-0433-5

[…] search for experimental B-cell and CD4+ T-cell epitopes homologous to HA2 fragments was performed in the Immune Epitope Database []. A search for possible CD8+ T-cell epitopes was conducted using the NetCTLpan 1.1 Server [] with default search parameters. Three-dimensional protein structures were visualized using the Chimera (1.5.3) program []. The Phyre2 open web resource was used for primary seq […]

library_books

Mapping HLA A2, A3 and B7 supertype restricted T cell epitopes in the ebolavirus proteome

2018
BMC Genomics
PMCID: 5780746
PMID: 29363421
DOI: 10.1186/s12864-017-4328-8

[…] er studies had elucidated putative T-cell epitopes of individual EBOV proteins [–] by use of bioinformatics tools, such as SYFPEITHI [, ], BIMAS [, ], IEDB [, ], NetMHCcons [], NetChop [], NetCTL [], NetCTLpan [], NetMHCpan [] and NetMHCIIpan []. However, the identification and analyses of T-cell epitopes from the complete ZEBOV proteome, especially in the context of HLA-supertype restriction and […]

call_split

HIV 1 adaptation to NK cell mediated immune pressure

2017
PLoS Pathog
PMCID: 5472325
PMID: 28582449
DOI: 10.1371/journal.ppat.1006361
call_split See protocol

[…] ding of peptides within 20 amino acids of the six polymorphisms (Env(17/20), Vpu(71/74), Gag(138) and Nef(9)) to HLA-C alleles, HLA-B*73:01 and HLA-B*46:01 and found 38 flanking binders. We then used NetCTLPan v1.1 to predict the ability of these peptides to be cleaved and transported with both the variant and the wildtype flanking region. We found that cleavage was only increased in the presence […]

library_books

In Silico Analysis of Epitope Based Vaccine Candidates against Hepatitis B Virus Polymerase Protein

2017
Viruses
PMCID: 5454424
PMID: 28509875
DOI: 10.3390/v9050112

[…] In a preselected environment, the IEDB recommend, MHC-NP, netCTLpan1.1, RANKPEP and netMHCpan3.0 server predicted the potent epitopes from the HBV polymerase sequence. To improve the accuracy of epitope prediction, we selected epitopes which were predicted b […]

library_books

The Value of Online Algorithms to Predict T Cell Ligands Created by Genetic Variants

2016
PLoS One
PMCID: 5019413
PMID: 27618304
DOI: 10.1371/journal.pone.0162808

[…] Predictions for HLA class I binding affinity, C-terminal proteasomal cleavage and TAP transporter efficiency are integrated in the combined algorithm NetCTLpan 1.1. In the algorithm, the weight on HLA class I binding affinity, C-terminal proteasomal cleavage and TAP transport efficiency is 0.750, 0.225 and 0.025 by default, respectively. Using the […]

call_split

In Silico Design of a Chimeric Protein Containing Antigenic Fragments of Helicobacter pylori; A Bioinformatic Approach

2016
PMCID: 4899534
PMID: 27335622
DOI: 10.2174/1874285801610010097
call_split See protocol

[…] In order to identify common epitopes that bind to both MHC class molecules as well as to count the total number of interacting MHC alleles, NetCTL and NetCTLpan were used. Such Softwares are predictors of T cell epitopes along a protein sequence. These tools at IEDB (www.cbs.dtu.dk/services/NetCTL predict the half maximal (50%) inhibitory concentrat […]

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NetCTLpan institution(s)
Department of Systems Biology DTU, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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