NetChop protocols

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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 in pipelines

 (3)
2016
PMCID: 5019413
PMID: 27618304
DOI: 10.1371/journal.pone.0162808

[…] 57 pairs of miha and allelic variants were compared for predicted proteasomal cleavage, tap affinity and in vivo immunogenicity (). no difference was observed in predicted proteasomal cleavage by netchop 3.1 (81% for miha versus 81% for allelic variants, p = 1.000) and tap affinity by tappred (40% high, 53% intermediate and 8% low affinity peptides for miha versus 47% high, 43% intermediate […]

2015
PMCID: 4463842
PMID: 25936538
DOI: 10.3892/mmr.2015.3673

[…] the cut-off score was adjusted to >20 for syfpeithi and t1/2>100 for bimas, and peptides matching these two criteria and which were shared by the two algorithms were selected. second, the netchop algorithm (http://www.cbs.dtu.dk/services/netchop/) was used to predict whether the selected peptides in the first step would be cleaved at the c-terminus. third, protein sequences […]

2015
PMCID: 4551310
PMID: 26175035
DOI: 10.1093/femsre/fuv031

[…] non-redundant at the protein level. hla alleles were used as targets for the epitope predictions. hla class i-restricted 9-mer epitopes were predicted using netmhccons1.1 (karosiene et al. ) and netchop3.1 c-terminal peptide processing algorithm (nielsen et al. ). hla class ii-restricted 15-mer epitopes were predicted using netmhciipan3.0 (karosiene et al. ). epitope selection used both weak […]


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NetChop in publications

 (43)
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] 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 […]

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 […]

PMCID: 5756538
PMID: 29203182
DOI: 10.1016/j.vaccine.2017.10.079

[…] from a subtype within the dataset, with a highest homology to the overall consensus was selected and included in conserved immunogens., 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, […]

PMCID: 5742119
PMID: 29312332
DOI: 10.3389/fimmu.2017.01848

[…] the endoplasmatic reticulum by the tap transporter and presented on the cancer cell surface. the process of proteasomal degradation can be predicted from a number of computational algorithms (e.g., netchop) but the accuracy of prediction remains to be improved. the expression of neoantigen epitopes with potential clinical relevance has successfully been demonstrated by mass spectrometry () […]

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

[…] 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 […]


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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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