List of experimental tools that aren't quite ready for primetime.
- RATE (Restrictor Analysis Tool for Epitopes):
is an automated method that can infer HLA restriction for a set of given epitopes from large
datasets of T cell responses in HLA typed subjects. The tool takes two data files, one containing
the alleles expressed by the subjects and the other containing the response of the peptides in
the subjects. The tool calculates the odds ratio and estimates its significance using Fisher's
exact test. It also calculates a parameter called relative frequency similar to odds ratio. The
tool was developed with a focus on class II alleles but can also be applied to class I alleles.
The Tepitool provides prediction of peptides binding to MHC class I and class II molecules. Tool
is designed as a wizard with 6 steps as described below. Each field (except sequences and alleles)
is filled with default recommended settings for prediction and selection of optimum
peptides. The input parameters can be adjusted as per your specific needs. You can go back to
previous steps to change your selection before submission of the job. Once you submit the job (at
the end of step-6), you will not be able to make any more changes and will have to start the
prediction all over again with updated input parameters.
The deimmunization tool is attempt to identify immunodominant regions in a given therapeutically
important protein, and suggest amino-acid substitutions that create non-immunogenic versions of
the proteins. So we have opted a two steps process; 1) In the first step, the deimmunization tool
will list all the immunogenic regions or peptides based on selected threshold. These peptides will
be generated from the protein with 15mer window size and 10mer overlap. 2) In the second step,
the user can select one or more peptides listed in the results and final result window will
display the non-immunogenic substitution of each selected peptides. The default threshold is
8.5 (which is difference in the median of percentile rank from 26 reference alleles set for
MHC class II). In the final result window, the tools will also take care of the fact that
non-immunogenic substitution in the immunogenic peptides, should not create new immunogenic site
in the neighboring peptides. Therefore, the result window will also display the effect of
substitution on the neighboring peptides.
- LYRA (Lymphocyte Receptor Automated Modelling):
The LYRA server predicts structures for either T-Cell Receptors (TCR) or B-Cell Receptors (BCR) using homology modelling. Framework templates are selected based on BLOSUM score, and complementary determining regions (CDR) are then selected if needed based on a canonical structure model and grafted onto the framework templates.
- Epitope Cluster Analysis Tool 2.0:
This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a group of sequences which have a sequence similarity greater than the minimum sequence identity threshold specified. User can also select the minimum and maximum length of peptide and also one of the three approaches for clustering of peptides.