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Epitope Prediction specifications

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Unique identifier OMICS_15043
Name Epitope Prediction
Interface Web user interface
Restrictions to use None
Input data The MHC-I type(s) to be tested, the length(s) of epitope to be tested, the DNA sequence(s).
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_15043
Name Epitope Prediction
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability No
Source code URL https://www.codeplex.com/MSCompBio/Release/ProjectReleases.aspx
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for Epitope Prediction

Epitope Prediction citations

 (6)
library_books

Genetic impact of vaccination on breakthrough HIV 1 sequences from the Step trial

2011
Nat Med
PMCID: 3053571
PMID: 21358627
DOI: 10.1038/nm.2316

[…] on gag was most robustly supported in both our phylogenetic and sieve analyses; yet, based on epipred-derived epitopes, the signal appeared to be mostly driven by differences in nef. given that the epitope prediction tools we used were trained on partially different datasets and assumptions, they rely on potentially different features of epitope-mhc binding; therefore we may expect […]

library_books

HLA Class I Binding of HBZ Determines Outcome in HTLV 1 Infection

2010
PLoS Pathog
PMCID: 2944806
PMID: 20886101
DOI: 10.1371/journal.ppat.1001117

[…] in the context of a*02); this represents a small and non-random fraction of the ∼2200 nonamer epitopes that could be bound by the alleles of the kagoshima cohort studied here (). therefore we used epitope prediction software to systematically predict htlv-1 epitopes. the epitope prediction software that we used has been extensively validated for a number of other organisms including hiv-1 […]

library_books

Epitope Discovery with Phylogenetic Hidden Markov Models

2010
Mol Biol Evol
PMCID: 2857806
PMID: 20089717
DOI: 10.1093/molbev/msq008

[…] this evidence can be combined using a phylogenetic hidden markov model (phylo-hmm) to make probabilistic epitope predictions based on sequence evolution. evolutionary information provides a means of epitope prediction, which is orthogonal to existing sequence- and structure-based methods. we demonstrate how this information can be integrated with other prediction methods within the phylo-hmm […]

library_books

Viral adaptation to immune selection pressure by HLA class I–restricted CTL responses targeting epitopes in HIV frameshift sequences

2010
PMCID: 2812535
PMID: 20065065
DOI: 10.1084/jem.20091808

[…] and responses exceeding three times the mean of negative wells. peptides were synthesized as listed in . specific epitopes with an hla-binding motif for the observed imprint were predicted using epitope prediction algorithms (available at http://atom.research.microsoft.com/bio/epipred.aspx [] and www.hiv.lanl.gov/content/immunology). in brief, for each hla-associated polymorphism, […]

library_books

HLA Associated Immune Escape Pathways in HIV 1 Subtype B Gag, Pol and Nef Proteins

2009
PLoS One
PMCID: 2723923
PMID: 19690614
DOI: 10.1371/journal.pone.0006687

[…] polymorphism does not fall within a known optimally-described epitope, we have not attempted to predict the likeliest epitope as has been done previously. this was done in order to avoid forcing an epitope prediction in the case where the hla association may be attributable to another mechanism (for example a processing escape mutation occurring distant from a published epitope), and also […]

library_books

Evidence of Differential HLA Class I Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV 1

2007
PLoS Pathog
PMCID: 1904471
PMID: 17616974
DOI: 10.1371/journal.ppat.0030094

[…] epitope anchor residue motif (using motifscan, http://hiv-web.lanl.gov/content/immunology/motif_scan/motif_scan) and/or a putative hla-restricted epitope identified by an independently validated ctl epitope prediction algorithm (epipred, http://atom.research.microsoft.com/bio/epipred.aspx []) based on scanning the cohort consensus sequence. again, associations falling within the “motif ± 3 aa […]


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Epitope Prediction institution(s)
Microsoft Research, Redmond, WA, USA
Epitope Prediction funding source(s)
This work was supported by an internship at Microsoft Research.

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