EpiToolKit—a web server for computational immunomics

Feldhahn, Magdalena; Thiel, Philipp; Schuler, M.; Hillen, Nina; Stevanović, Stefan; Rammensee, Hans‐Georg; Kohlbacher, Oliver

doi:10.1093/nar/gkn229

Cited by 22 publications

(16 citation statements)

References 19 publications

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“…OptiTope offers three kinds of thresholds: user-defined, percentage (16) and halfmax (16). The percentage thresholds are calculated based on a large set of naturally occurring peptides.…”

Section: Methodsmentioning

confidence: 99%

“…The corresponding probabilities will be employed for the next query. Alternatively, the MHC alleles can be selected manually from an expandable allele tree (16) or by pasting a list of alleles.In this step, a list of the selected MHC alleles along with probabilities (default values or values retrieved from the NCBI dbMHC database, respectively) is given. These probabilities can either be modified manually or they can be replaced by population or geographic area-specific probabilities from the NCBI dbMHC database via the advanced options.…”

Section: Web Interfacementioning

confidence: 99%

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OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines

Toussaint

Kohlbacher

2009

Nucleic Acids Research

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Epitope-based vaccines (EVs) have recently been attracting significant interest. They trigger an immune response by confronting the immune system with immunogenic peptides derived from, e.g. viral- or cancer-related proteins. Binding of these peptides to proteins from the major histocompatibility complex (MHC) is crucial for immune system activation. However, since the MHC is highly polymorphic, different patients typically bind different repertoires of peptides. Furthermore, economical and regulatory issues impose strong limitations on the number of peptides that can be included in an EV. Hence, it is crucial to identify the optimal set of peptides for a vaccine, given constraints such as MHC allele probabilities in the target population, peptide mutation rates and maximum number of selected peptides. OptiTope aims at assisting immunologists in this critical task. With OptiTope, we provide an easy-to-use tool to determine a provably optimal set of epitopes with respect to overall immunogenicity in a specific individual (personalized medicine) or a target population (e.g. a certain ethnic group). OptiTope is available at http://www.epitoolkit.org/optitope.

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“…OptiTope offers three kinds of thresholds: user-defined, percentage (16) and halfmax (16). The percentage thresholds are calculated based on a large set of naturally occurring peptides.…”

Section: Methodsmentioning

confidence: 99%

Section: Web Interfacementioning

confidence: 99%

OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines

Toussaint

Kohlbacher

2009

Nucleic Acids Research

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“…Based on this knowledge, various algorithms have been developed for predicting the propensity of TAA-derived sequences to bind specific MHC molecules 25 . Later on, this approach has been combined with the SEREX technology, allowing the identification of additional important TAAs.…”

Section: Clinical Status Of Immunotherapy—melanoma and Prostate Cancermentioning

confidence: 99%

Implementing combinatorial immunotherapeutic regimens against cancer

2014

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Harnessing the host immune system to eradicate cancer has a high therapeutic potential. One paradigm of anticancer immunotherapy is represented by allogeneic stem cell transplantation. In this setting, the host must be conditioned prior to transplantation, allowing for engraftment and subsequent graft-vs.-tumor reactivity. Conditioning may also be a prerequisite for the efficacy of other immunotherapeutic regimens. In particular, tumor debulking followed by conditioning (aimed at blocking endogenous inhibitory stimuli, for instance upon the depletion of regulatory T cells or the inhibition of immune checkpoints) and subsequent immunization (for instance by means of patient-tailored vaccines) based on innovative adjuvants (such as RIG-I ligands) may allow for the elicitation of superior antitumor immune responses. Repetitive boosting might then maintain immunosurveillance. An intense wave of investigation on the optimal timing of immunostimulatory interventions with respect to the administration of immunogenic chemotherapeutics and on the use of small drugs that promote efficient antitumor immune responses will end up in the generation of highly effective immunotherapeutic anticancer regimens.

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“…An example of an application based on FRED is EpiToolKit (www.epitoolkit.org, Feldhahn et al , 2008; Toussaint and Kohlbacher, 2009). Only the web-based user interface and the data management in the web server had to be newly implemented.…”

Section: Applicationsmentioning

confidence: 99%

FRED—a framework for T-cell epitope detection

et al. 2009

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Summary: Over the last decade, immunoinformatics has made significant progress. Computational approaches, in particular the prediction of T-cell epitopes using machine learning methods, are at the core of modern vaccine design. Large-scale analyses and the integration or comparison of different methods become increasingly important. We have developed FRED, an extendable, open source software framework for key tasks in immunoinformatics. In this, its first version, FRED offers easily accessible prediction methods for MHC binding and antigen processing as well as general infrastructure for the handling of antigen sequence data and epitopes. FRED is implemented in Python in a modular way and allows the integration of external methods.Availability: FRED is freely available for download at http://www-bs.informatik.uni-tuebingen.de/Software/FRED.Contact: feldhahn@informatik.uni-tuebingen.de

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EpiToolKit—a web server for computational immunomics

Cited by 22 publications

References 19 publications

OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines

OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines

Implementing combinatorial immunotherapeutic regimens against cancer

FRED—a framework for T-cell epitope detection

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