NetMHCstab protocols

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NetMHCstab specifications

Information


Unique identifier OMICS_21804
Name NetMHCstab
Interface Web user interface
Restrictions to use None
Input data A single sequence or several sequences.
Input format FASTA,PEPTIDE
Output data Height columns: Residue number, HLA Allele, Peptide sequence, Protein identifier, Prediction score, Affinity as IC50 value in nM, %Random - %Rank of prediction score to a set of 1000.000 random natural 9mer peptides and Binding level.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline NetChop Team <>
  • person_outline Morten Nielsen <>

Additional information


http://www.cbs.dtu.dk/services/NetMHCstab/instructions.html

Publication for NetMHCstab

NetMHCstab in pipeline

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

[…] as available at http://www.cbs.dtu.dk/biotools/mhcmotifviewer/human_alleles.html []., we also compared miha and their allelic variants in predicted stability of the peptide-hla class i complex by netmhcstab 1.0 (). hla class i restriction alleles were available for 41 pairs of miha and allelic variants. for 7 pairs with polymorphic amino acids at anchor residues, predicted stability […]


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NetMHCstab in publications

 (6)
PMCID: 5597684
PMID: 28589207
DOI: 10.1007/s00251-017-1004-8

[…] to be more stably bound to mhc-i molecules than non-immunogenic peptides, suggesting to focus on stability rather than affinity as a determinant for peptide immunogenicity. in the wake of this, the netmhcstab and netmhcstabpan servers were recently established (jørgensen et al. ; rasmussen et al. ). unfortunately, these servers have so far only been trained with human data, and could therefore […]

PMCID: 5055684
PMID: 27717382
DOI: 10.1186/s12967-016-1042-2

[…] of binding to hla- a*01:01, a*02:01, a*03:01 and b*08:01 molecules (fig. ). epitope candidates were only selected if identified by all programs according to their predictive scores (table ). the netmhcstab [], netmhc, and netmhccons (fig. ) prediction algorithms provided by the center for biological sequence analysis (cbs, http://www.cbs.dtu.dk) was used to predict the stability of pmhc […]

PMCID: 5019413
PMID: 27618304
DOI: 10.1371/journal.pone.0162808

[…] for hla class i, stability of the peptide-hla class i complex, proteasomal cleavage at the c-terminus, affinity for tap and in vivo immunogenicity, the online available algorithms netmhcpan 2.8[], netmhcstab 1.0 [], netchop 3.1 [], tappred [] and the mhc i immunogenicity tool from the immune epitope database(iedb) [] were used, respectively. in addition, netctlpan 1.1 [] was used to integrate […]

PMCID: 4955262
PMID: 27439771
DOI: 10.1186/s12859-016-1150-2

[…] the 20,041 proteins. after removing the 9-mers that contain non-standard amino acids, a set of 11,118,076 peptides remains., potential peptide-hla complexes are identified using a webserver called netmhcstab (version 1.0) []. netmhcstab webserver employs a neural network based machine learning model to predict the binding affinity of a peptide and hla allele. the predicted binding affinity […]

PMCID: 4654883
PMID: 26589500
DOI: 10.1186/s13073-015-0245-0

[…] by considering the binding stability of the peptide–hla complex []. as there are only few data available for the binding stability, there has only been an account of a single tool published so far (netmhcstab [])., hla class ii ligand prediction is more difficult than class i prediction owing to the unknown position of the binding core within the generally longer peptides. as for hla class i, […]


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NetMHCstab institution(s)
Department of Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark; Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, San Martin, Buenos Aires, Argentina
NetMHCstab funding source(s)
Supported in whole or in part with funds from the National Institutes of Health, under Contracts No. HHSN272200900045C and HHSN272201200010C.

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