NetMHCcons protocols

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NetMHCcons specifications


Unique identifier OMICS_17787
Name NetMHCcons
Interface Web user interface
Restrictions to use None
Input data A list of peptides or a protein.
Input format FASTA
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes


  • person_outline Edita Karosiene <>

Publication for NetMHCcons

NetMHCcons in pipelines

PMCID: 5267949
PMID: 28149040
DOI: 10.6026/97320630012082

[…] since naturally acquired antibodies generated against them inhibit erythrocyte invasion and in some cases result in the clinical protection from disease. we thus used in silico tools (bcpreds, netmhccons and netmhciipan 3.0) to predict b-cell epitopes (bces) and t-cell epitopes (tces) in two merozoite invasion proteins, eba175-rii and rh5. initially, we validated these tools using csp […]

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

[…] ted in the 53 ebolavirus genomes that were 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 […]

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NetMHCcons in publications

PMCID: 5946011
PMID: 29780384
DOI: 10.3389/fimmu.2018.00912

[…] leucine to isoleucine residue were identified, both matches were retained in the dataset. putative hla class i or ii restriction and binding affinity of identified peptides was predicted using the netmhccons, netmhc4.0, or netmhcii online algorithms (found at (). sequence logos of identified peptides were produced using the default settings for shannon type […]

PMCID: 5915591
PMID: 29691454
DOI: 10.1038/s41598-018-24674-8

[…] based on the clustalw algorithm. the protein sequence of reca (agw25358) and flid (wp_001110738) were retrieved from genbank and subjected for b-cell and t-cell epitope prediction using bcpred, netmhccons and netmhcii. for peptide - mhc binding analysis, a panel of alleles were selected, which account for 97% of hla allelic variants in most ethnicities. netmhccons and netmhcii were used […]

PMCID: 5928857
PMID: 29618661
DOI: 10.1172/jci.insight.98575

[…] matrix method (smm), smm with a peptide/mhc binding energy covariance matrix (smmpmbec), scoring matrices derived from combinatorial peptide libraries (comblib_sidney2008), consensus, netmhcpan, netmhccons, pickpocket, and netmhcstabpan (, ). the list of peptides was filtered to include 8- to 14-mer peptides that bind to hla-a, hla-b, and hla-c allotypes. iedb recommended was the default […]

PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] mhc class i binding predictions were generated through pvacseq using netmhc v3.4, as well as five other algorithms from the immune epitope database and analysis resource (iedb, netmhc, netmhccons, netmhcpan, pickpocket, smm, and smmpmbec. predictions were retained if the median score had an ic50 < 500 and better binding of the mutant peptide than the wild type (fold-change > […]

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

[…] and netmhc [], 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 […]

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NetMHCcons institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
NetMHCcons funding source(s)
This work was supported by two NIH (National Institute of Health) grants (contract no. HHSN272200900045C, and contract no. HHSNN26600400006C).

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