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MHCPEP specifications

Information


Unique identifier OMICS_04571
Name MHCPEP
Restrictions to use None
Maintained No

Publication for MHCPEP

MHCPEP citations

 (8)
library_books

HLA class I molecular variation and peptide binding properties suggest a model of joint divergent asymmetric selection

2016
Immunogenetics
PMCID: 4911380
PMID: 27233953
DOI: 10.1007/s00251-016-0918-x

[…] structures of the PBR) (Francisco et al. ; Sidney et al. ). As a crucial question was to characterize both MHC ligands and peptide motifs involved in peptide binding, diverse database resources like MHCPEP (Brusic et al. ), SYFPEITHI (Rammensee et al. ), and IEDB (Peters et al. ; Vita et al. ) were also created. In addition, because the very high level of polymorphism observed in the PBR makes th […]

library_books

Structural Properties of MHC Class II Ligands, Implications for the Prediction of MHC Class II Epitopes

2010
PLoS One
PMCID: 3012731
PMID: 21209859
DOI: 10.1371/journal.pone.0015877

[…] ds, a simple model was created which integrated the MHC-II binding affinity with a structural feature or surface exposure as described by Eq.(1).(1)where x is an MHC class II ligand likelihood score, MHCpep represents the MHC binding affinity and is the mean value of a structural class (i.e. α-helix, β-strand, coil or RSA) for the peptide. Brute force grid search was used to identify the value of […]

library_books

Predicting MHC class I epitopes in large datasets

2010
BMC Bioinformatics
PMCID: 2836306
PMID: 20163709
DOI: 10.1186/1471-2105-11-90

[…] e context in which they are immunogenic. The Los Alamos HIV Molecular Immunology Database [], focuses on a restricted dataset. FIMM [], is of modest size and solely focuses on cellular immunology and MHCPEP [], while still widely used, has not been updated since 1998. While MHCBN [] and AntiJen [,] contain peptide entries that are not contained in IEDB, IEDB has more entries than any other existin […]

library_books

Prediction of HLA DQ8 β cell peptidome using a computational program and its relationship to autoreactive T cells

2009
Int Immunol
PMCID: 2686615
PMID: 19461125
DOI: 10.1093/intimm/dxp039

[…] wo computational programs are publicly available for predicting peptides bound to DQ8 molecules: RankPep and MHC2Pred (–). RankPep derived a weight matrix profile using DQ8-bound peptides () from the MHCPEP database (). MHC2Pred () applied a matrix optimization technique, which is motif less on the DQ8 peptides from the MHCBN and JenPep databases (, ), and employed a support vector machine approac […]

library_books

On Evaluating MHC II Binding Peptide Prediction Methods

2008
PLoS One
PMCID: 2533399
PMID: 18813344
DOI: 10.1371/journal.pone.0003268

[…] des in the non-binders category. The result is a dataset of weighted instances.Thus, from each MHC-II benchmark dataset, we generated five versions summarized below:Three datasets of unique peptides, MHCPEP-UPDS, MHCBN-UPDS, and IEDB-UPDS extracted from MHCPEP, MHCBN, and IEDB, respectively after eliminating short peptides consisting of fewer than 9 residues, unnatural peptides, peptides with grea […]

library_books

Strength in numbers: achieving greater accuracy in MHC I binding prediction by combining the results from multiple prediction tools

2007
Immunome Res
PMCID: 1847428
PMID: 17381846
DOI: 10.1186/1745-7580-3-5

[…] dict binding affinity or in the data used to train the model. The tools tested are as follows: Bimas [], Rankpep [], SYFPEITHI [], NetMHC 2.0 ANN and NetMHC 2.0 Matrix [,,], SVMHC SYFPEITHI and SVMHC MHCPEP [], HLA Ligand [], Predep [], SMM [], MHCPred (position only) and MHCPred (interactions) [,], Multipred HMM and Multipred ANN [-], ARB Matrix [], and a locally implemented logistic regression-b […]

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MHCPEP institution(s)
The Walter and Eliza Hall Institute, Parkville, Victoria, Australia

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