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Protocols

NetChop specifications

Information


Unique identifier OMICS_05749
Name NetChop
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Version 3.1
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline NetChop Team

Publications for NetChop

NetChop citations

 (52)
call_split

Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

2018
Cancer Sci
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498
call_split See protocol

[…] nicity in individual patients, and it has been reported that peptide–HLA complex stability might have a better correlation with the immunogenicity of the peptides. Some computational methods, such as NetChop and NetCTL, focus on predicting antigen processing and peptide transport processes., Structural‐based approaches are also important to predict the orientation of a mutated amino acid that is […]

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

[…] [], among others. Earlier 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-sup […]

call_split

The generation of a simian adenoviral vectored HCV vaccine encoding genetically conserved gene segments to target multiple HCV genotypes

2018
Vaccine
PMCID: 5756538
PMID: 29203182
DOI: 10.1016/j.vaccine.2017.10.079
call_split See protocol

[…] Prediction of proteasomal cleavage sites was run using server NetChop 3.1, (version C-term 3.0). Epitope prediction analysis was run using online epitope prediction programs NetMHC, Syfpeithi and BIMAS with a cut-off for strong epitope binders of <0.5, >20, and […]

library_books

Neoantigen Targeting—Dawn of a New Era in Cancer Immunotherapy?

2017
Front Immunol
PMCID: 5742119
PMID: 29312332
DOI: 10.3389/fimmu.2017.01848

[…] en the mutational burden in tumors and the observed response came from checkpoint inhibitor studies using either PD-1/PD-L1 or CTLA-4 inhibitors. After tumor exome sequencing and data processing with NetChop and NetMHC algorithms, van Rooij et al. showed the expansion of a T cell response directed against a mutated version of ATR (ataxia teleangiectasia and rad3 related) in a melanoma patient afte […]

library_books

Exploring dengue genome to construct a multi epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection

2017
Sci Rep
PMCID: 5569093
PMID: 28835708
DOI: 10.1038/s41598-017-09199-w

[…] icial neural networks while TAP transport efficiency was achieved by an approach based on weight matrix, while C-terminal proteasomal cleavage site was predicted by the artificial neural network from NetChop 3.1 server. Scores of all three predictions were merged together and sensitivity or specificity values can be achieved by the conversion of the threshold from the merged score. During CTL epit […]

library_books

Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

2017
Genome Med
PMCID: 5442873
PMID: 28539123
DOI: 10.1186/s13073-017-0434-0

[…] predicted to be generated by cleavage in proteasomes, the list of neoantigens was filtered to include only peptides with predicted C-terminal cleavage sites using the stand-alone software package of NetChop 3.1 []. When summarizing the number of neoantigens per tumor, peptides predicted to bind to several HLA alleles were counted only once. […]

Citations

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NetChop institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, Netherlands

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