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Protocols

NetMHCIIpan specifications

Information


Unique identifier OMICS_06759
Name NetMHCIIpan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Edita Karosiene

Publication for NetMHCIIpan

NetMHCIIpan citations

 (84)
library_books

Specific β Turns Precede PPIIL Structures Binding to Allele Specific HLA DRβ1* PBRs in Fully Protective Malaria Vaccine Components

2018
PMCID: 5898157
PMID: 29682500
DOI: 10.3389/fchem.2018.00106

[…] as led to advances regarding knowledge about protein and peptide 3D structure and knowledge of the immune system molecules involved in major histocompatibility complex (http://www.cbs.dtu.dk/services/NetMHCIIpan/) Class I and Class II (HLA-DRβ*) antigen presentation to the T-cell receptor (TCR) to form the MHCII-peptide-TCR complex or immunological synapse to induce an appropriate immune response […]

call_split

Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma

2018
JCI Insight
PMCID: 5928857
PMID: 29618661
DOI: 10.1172/jci.insight.98575
call_split See protocol

[…] ed us to choose between 7 currently implemented MHC class II binding prediction methods: IEDB Recommended, Consensus method, Comblib, NN-align (netMHCII-2.2), SMM-align (netMHCII-1.1), Sturniolo, and NetMHCIIpan (, ). The list of peptides was filtered to include 15-mer peptides that bind to HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DPA1, HLA-DPB1, HLA-HQA1, and HLA-DQB1 allotypes. The default se […]

call_split

Homology modeling and epitope prediction of Der f 33

2018
Braz J Med Biol Res
PMCID: 5875910
PMID: 29561952
DOI: 10.1590/1414-431X20186213
call_split See protocol

[…] T cell epitopes were predicted by identifying the binding of peptides to MHC molecules with NetMHCII 2.2 () and NetMHCIIpan-3.1 ().NetMHCII 2.2 uses artificial neuron networks to predict binding of epitope peptides to HLA-DQ alleles in regions of HLA-DQA10101-DQB10501, HLA-DQA10102-DQB10602, HLA-DQA10301-DQB103 […]

library_books

PIRCHE II Is Related to Graft Failure after Kidney Transplantation

2018
Front Immunol
PMCID: 5844930
PMID: 29556227
DOI: 10.3389/fimmu.2018.00321

[…] For all HLA mismatches, we determined the number of donor mismatched HLA-derived peptides that can be presented by recipient HLA-DRB1 (PIRCHE-II) as described previously (). Briefly, the NetMHCIIpan 3.0 algorithm was used to predict the nonameric binding cores of donor mismatched HLA-derived peptides that can bind to recipient HLA-DRB1. Relevant HLA-DRB1 binders were defined as peptid […]

library_books

Frequency of Interferon Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T Cell Epitopic Context

2018
J Immunol Res
PMCID: 5821972
PMID: 29577052
DOI: 10.1155/2018/7685371

[…] 0.0%), DQA1∗0501 (47.3%), DQB1∗0201 (33.7%), DQB1∗0301 (39.3%), DQB1∗0501 (20.3%), and DQB1∗0602-08 (36.0%) []. Analysis of binding of these HLA II molecules with HCV core-derived peptides done using NetMHCIIpan program included the total of 275 alleles. None of the HLA II DRB1 alleles prevalent in Russia were predicted to bind any aa fragment within the consensus HCV 1b core sequence spanning aa […]

library_books

Immune monitoring and TCR sequencing of CD4 T cells in a long term responsive patient with metastasized pancreatic ductal carcinoma treated with individualized, neoepitope derived multipeptide vaccines: a case report

2018
J Transl Med
PMCID: 5801813
PMID: 29409514
DOI: 10.1186/s12967-018-1382-1

[…] dicted to bind to HLA-B44 and show identical amino acids in anchor positions 2 (E) and 7 (R) []. Hydrophobic peptides 2 and 3 both bind to CD1d. Peptides 1 and 2 with the highest SYFPEITHI scores and NetMHCIIpan predictions induced most of the detectable CDR3 sequences and the highest number of clones (Table ).Three germline encoded CDR3 sequences (i.e. recombination of VD(J) gene segments without […]

Citations

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

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