Antigenicity and Immunogenicity of B-Epitopes
EpiQuest-B is a program that predicts the relative antigenicity of linear B-cell epitopes independently of domain accessibility on the surface of the folded mature protein. The program evaluates the relative potential of the protein sequences to elicit humoral immune response based on the composition and relative positioning of the amino acids in sequence.
EpiQuest-IM allows the user to evaluate the potential immunogenicity of the protein sequences when the native protein is used for immunization, and some areas of it are not exposed, with some - better accessible by the immune system (B-cell receptor).
B-scanner allows the user to analyse and compare the relative antigenicity of large collections of linear peptide B-epitopes, for example, selected by some other criteria - by their uniqueness (complexity), exposure at the surface of the molecule, hydrophobicity etc. The program can analyse large databases of epitopes, selecting the best (or best fragments of the required size) from the analysed sequences. The program employs the same algorithm and matrices as EpiQuest-B.
Prediction and Immunodominance of CTL epitopes
EpiQuest-T locates the areas of potential CTL epitopes and their relative "strength" based on the context of amino acid in linear protein sequence ( the analysed area). The prediction of dominant CTL epitopes is very accurate and is MHC-restricted. We constantly release new analysis matrices for various haplotypes.
Based on the same algorithm and MHC-specific matrices as EpiQuest-T, T-Scanner lets the user compare the antigenicity ("strength") of multiple epitope sequences, isolated by some other way. Originally, the program was developed for functional ranking of the epitopes isolated from a donor's cells, but can also be successfully used to rank the epitopes predicted by other programs (i.e. by approaches based on prediction proteosomal cleavage or MHC-binding)
Surface accessibility of protein domains
The program EpiQuest-A analyses the probability of proteins domain exposure at the surface of the folded protein. The program is designed to select the domains (and peptide epitopes) that will be accessible for antibody binding at the surface of the intact protein molecule.
Complexity of protein domains
As the peptide epitopes (or molecule's domain) used as antigen (for making antibody or within the vaccine) should elicit a specific immune response, the program EpiQuest-C analyses the level of complexity and potential immunological uniqueness for domains of the protein on the basis of its primary sequence. It can be also used to locate organised and disorganized areas of the protein in evolutionary studies.
Based on the same algorithm and the values matrix as EpiQuest-C, the program allows screening large numbers of peptide epitopes (B or T) for their relative (or absolute) uniqueness.
Hydropathy of protein domains
The program allows the user to build the hydropathy profile of the protein sequence based on six different value matrices for hydrophobic and hydrophilic amino acids. The matrices were adjusted to deliver the comparable results.
Stability & Mutability of protein domains
A program to evaluate the probability of spontaneous mutations in various regions in the absence of selective pressure (based on probabilities of a single individual amino acid replacements). Allows the user to select regions most prone to stability in fast replicating and evolving sequences accumulating point mutations (i.e. viral proteins).
Statistics for Protein Sequence
A simple tool to review the amino acid composition of the protein or peptide sequence of interest. Provides statistics for types of amino acids in a sequence or a collection of sequences.
Protein Charge and pI point
A utility program to predict the pI (isoelectric) point of a peptide/protein, as well as its charge at different pH. Created for working with peptides, although quite extensively tested with protein sequences as well. On the set of proteins with experimentally determined pI points, InCharge performs better than its analogues and competitors. This was true for proteins ranging in size from 5 to 200kD.