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OptiTope specifications

Information


Unique identifier OMICS_11284
Name OptiTope
Interface Web user interface
Restrictions to use None
Input data A list of multiple sequence alignments in FASTA format, a list of epitopes of equal length, one epitope per line, and a table of epitopes and their immunogenicities with respect to specific alleles.
Computer skills Basic
Stability Stable
Maintained No

Maintainer


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Publications for OptiTope

OptiTope citations

 (6)
library_books

Designing string of beads vaccines with optimal spacers

2016
Genome Med
PMCID: 4728757
PMID: 26813686
DOI: 10.1186/s13073-016-0263-6

[…] itope prediction [–]. Different algorithms have been suggested as well for selecting an optimal set of epitopes for EV design, each emphasizing different aspects of EVs [–]. Among these approaches is OptiTope, a mathematical framework that relies on integer linear programming, which can easily be adapted to many different settings and types of EVs [, ].Nevertheless, the stability and delivery of E […]

library_books

Genome Wide Prediction of Vaccine Candidates for Leishmania major: An Integrated Approach

2015
PMCID: 4670862
PMID: 26681959
DOI: 10.1155/2015/709216

[…] thermore, CTL epitopes prediction was carried out using NetCTL1.2 [, ] tool integrating predictions of proteasomal cleavage, TAP transport efficiency, and 12 MHC class I supertypes' binding. Finally, OptiTope (http://etk.informatik.uni-tuebingen.de/optitope) was used to determine good vaccine epitopes called the optimal set of epitopes from top scoring naturally processed T cell epitopes, for each […]

library_books

Sequence based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds

2012
BMC Immunol
PMCID: 3552980
PMID: 23227878
DOI: 10.1186/1471-2172-13-67

[…] Candidate epitopes chosen for “optimal” vaccines for Caucasians and Zulus, respectively, from the OptiTope analyses described above, were then tested using the South African white and black populations. Local population data was placed into the IEDB population coverage web application as before.Re […]

library_books

Vaccines: From Empirical Development to Rational Design

2012
PLoS Pathog
PMCID: 3493475
PMID: 23144616
DOI: 10.1371/journal.ppat.1003001

[…] absolutely essential to constantly improve predictions , . Examples for such databases are IEDB , or SYFPEITHI, which only lists experimentally validated natural MHC–peptide complexes , . The tools OptiTope , and NetMHCcons , select for epitope peptides from specific MHC alleles or sets of MHC alleles as they occur naturally in individuals of a certain population. This is achieved by choosing […]

library_books

Systems biology in vaccine design

2012
PMCID: 3815789
PMID: 22189033
DOI: 10.1111/j.1751-7915.2011.00321.x

[…] d for the formulation of multi‐epitope vaccines with broad population coverage, using HLA binding profile matrices coupled to filtering for immunoproteasome cleavage using probabilistic modelling (). OptiTope offers a step‐by‐step interface to assist immunologists in designing epitope‐based vaccines. It relies on an original algorithm that maximizes the overall immunogenicity of an epitope set (). […]

library_books

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools a compass in the land of biomarker discovery

2011
J Transl Med
PMCID: 3189883
PMID: 21929757
DOI: 10.1186/1479-5876-9-155

[…] tes, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices Website: http://www.gene-regulation.com/pub/databases.html Name: OptiTopeComment:OptiTope aims at assisting immunologists in designing epitope-based vaccines. It is an easy-to-use tool to determine a provably optimal set of epitopes with respect to overall immunogenicity in a spec […]

Citations

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OptiTope institution(s)
Division for Simulation of Biological Systems, Wilhelm Schickard Institute for Computer Science, Center for Bioinformatics Tübingen, Eberhard-Karls-Universität Tübingen, Germany

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