NetMHCpan protocols

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NetMHCpan specifications


Unique identifier OMICS_03503
Name NetMHCpan
Alternative names NetMHCpan-3.0, NetMHCpan 4.0
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.4
Stability Stable
Maintained Yes


  • person_outline Morten Nielsen <>

Publications for NetMHCpan

NetMHCpan in pipelines

PMCID: 5450251
PMID: 28584450
DOI: 10.6026/97320630013094

[…] identified from hla matchmaker program available at, using the identified consensus aa sequences as the input, t-cell epitopes that bind to mhc class i were predicted using netmhcpan 3.1 online server. this program predicts binding of peptides to any mhc molecule of known sequence using artificial neural networks (anns) []. the epitopes of 9-mer and 10-mer lengths […]

PMCID: 5602290
PMID: 28943728
DOI: 10.6026/97320630013231

[…] to design a candidate t-cell epitope vaccine using immunoinformatics strategies. the peptide epitopes that bind to class i hla supertypes and stimulate t-cell immune responses are predicted by the netmhcpan software. we aimed to identify candidate tcell epitope(s) conserved in all 5 hantavirus genotypes (hantaan, dobrava-belgrade, seoul, gou and amur) causing hfrs. the epitopes that bind […]

PMCID: 5602290
PMID: 28943728
DOI: 10.6026/97320630013231

[…] was used for further analysis to identify t-cell epitopes., we selected the class i mhc supertype representative alleles (n=12) for the prediction of specific t-cell epitopes as available in the netmhcpan 3.1 online prediction server program []. the epitopes of 9-mer length (nonamer) was derived with the default threshold for strong binding and weak binding in terms of percent rank. strong […]

PMCID: 4852757
PMID: 27147821
DOI: 10.4137/BBI.S38378

[…] using paproc-i tools (, while the transport antigen presentation (tap) binding was predicted by using tappred server (, propred and netmhcpan servers were used to identify the bond region on the class i hla of the antigen.,, the selected epitopes were further analyzed their conformation and stability by performing epitope […]

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NetMHCpan in publications

PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] (v4.0.8) was run for each patient and allele combination using 9mer epitopes generated from 17-mer peptides surrounding each missense mutation, and using mhc binding predictions generated by netmhcpan (v2.8) []. for each resulting neoepitope from pvac-seq, additional metrics were applied as described below. note that for the purposes of this study, only epitopes resulting from missense […]

PMCID: 5898157
PMID: 29682500
DOI: 10.3389/fchem.2018.00106

[…] αr (3/16), via1 and iv3 β-turn (one each); interestingly, (6/16) had random structures (nf) in the preceding region, though sequence pbr binding by 1h-nmr had αr structures (theoretically, the netmhcpan 3.1 platform predicted that only 3/16 had some hla-dr binding) (figure ). such data clearly correlated 3d structural conformation with particular immunological outcomes where impips […]

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

[…] stabilized 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 […]

PMCID: 5885379
PMID: 29618380
DOI: 10.1186/s40425-018-0331-0

[…] were based on predicted ability to bind mhci. both wt and snv 8-11mer peptides were based on the length and frame of the top predicted mhci binding minimal 8-11mer snv peptide identified using netmhcpan v2.8 server. netmhcpan, was used to calculate predicted h2-kd, h2-dd, and h2-ld mhci binding scores for all possible wt and snv 8mers, 9mers, 10mers, and 11mers that include the mutation […]

PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] each sample, recoding sites (detected by the he analysis) inside peptides that have at least one window (see ) with strong affinity to the sample-predicted hla alleles were selected according to the netmhcpan4.0 () predictions. a recoding event was considered to have an affinity-enhancing effect if the edited version of the peptide, for all windows on average, had a higher affinity (of at least […]

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NetMHCpan institution(s)
Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina

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