Goals |
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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 specific individual or a target population.
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Method |
OptiTope maximizes overall immunogenicity with respect to the user's requirements.
The overall immunogenicity of an epitope set depends on the immunogenicity
of its components with respect to the MHC alleles in the target population. Furthermore, the
contribution of an MHC allele directly depends on its probability of occuring within the target
population. More common alleles are weighted more than uncommon ones. Thus, the overall immunogenicity
of a set of epitopes can be derived as the sum of the components' immunogenicities weighted by the
probability of the respective MHC allele.
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Notice: This (commonly made) assumption of independence between epitopes poses a simplification. Lacking an accurate model of the interplay
of different epitopes, however, it seems like the best assumption one can make.
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Algorithmic basis: Toussaint et al.,
2008, PLoS Comput Biol 4(12):e1000246.
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Usage |
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Step-by-step the user is asked to enter sequences of known antigens, information on the target individual or population,
and additional requirements on the epitope set to be selected.
Navigation through the individual steps is guided by this navigation bar at the top of each site.
The navigation bar indicates the current step and contains corresponding instructions.
Furthermore,
it provides access to a more detailed help page.
The color of the step in the navigation bar corresponds
to the heading colors of the documentation and the help page.
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Target Antigens |
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In this step the antigenic sequences are entered. You can upload a file or paste
the sequences. Easy access to sample data is provided.
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Target Population |
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In this step the MHC alleles of interest and their probabilities in the target population
are entered. You can choose from a list of populations or population areas obtained from
the NCBI dbMHC, select alleles from
an allele tree, or enter them manually.
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Constraints |
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In this step a brief summary of the input data is given and the
constraints on the sought set of epitopes are selected. You can choose from a
list of available constraints and can adapt them to your requirements.
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Results |
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In the final step the results are displayed.
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In each step the corresponding help page including helpful information can be accessed.
To access the help page click on this button:
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Tutorial |
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An
introductory tutorial shall help new users to learn how to use the OptiTope web server.
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OptiTope is a service of the
Division for Simulation of Biological Systems
at the Eberhard-Karls-Universität, Tübingen.
It is incorporated into the SBS EpiToolKit, a website provided
by our group to support immunological research.
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