EpiQuest-B | EpiQuest-A | EpiQuest-IM | EpiQuest-C |EpiQuest-T | EpiQuest-H | EpiQuest-M | In Charge | EpiStat
Antigenicity and Immunogenicity of B-Epitopes
EpiQuest-B
EpiQuest-B is a program designed to predict the relative antigenicity of linear B-cell epitopes, regardless of domain accessibility on the surface of the folded mature protein. This program assesses the protein sequences' relative potential to stimulate humoral immune responses based on the composition and relative positioning of amino acids within the sequence.
EpiQuest-IM
EpiQuest-IM enables users to assess the potential immunogenicity of protein sequences, particularly when the native protein is utilized for immunization. It accounts for areas of the protein that may not be exposed, with some regions being better accessible to the immune system, particularly the B-cell receptor.
B-Scanner
The B-scanner tool enables users to analyze and compare the relative antigenicity of extensive collections of linear peptide B-epitopes. These epitopes may be selected based on various criteria such as uniqueness (complexity), surface exposure on the molecule, hydrophobicity, and more. The program is capable of analyzing large databases of epitopes, identifying the best candidates or optimal fragments of the required size from the analyzed sequences. Utilizing the same algorithm and matrices as EpiQuest-B, B-scanner ensures robust and reliable epitope analysis.
Prediction and Immunodominance of CTL epitopes
EpiQuest-T
EpiQuest-T is designed to identify potential CTL epitopes and assess their relative "strength" within the context of amino acids in linear protein sequences, focusing on the analyzed region. The program offers highly accurate predictions of dominant CTL epitopes that are MHC-restricted. Additionally, we consistently update the analysis matrices to accommodate various haplotypes, ensuring comprehensive coverage and accuracy in epitope prediction.
T-Scanner
Utilizing the same algorithm and MHC-specific matrices as EpiQuest-T, T-Scanner allows users to compare the antigenicity ("strength") of multiple epitope sequences isolated through various methods. Originally developed for functional ranking of epitopes isolated from donor cells, the program is also effective in ranking epitopes predicted by other programs, such as those based on proteosomal cleavage prediction or MHC-binding approaches.
Surface accessibility of protein domains
Complexity of protein domains
EpiQuest-C
Since peptide epitopes or molecular domains used as antigens, either for antibody production or within vaccines, should evoke specific immune responses, the EpiQuest-C program analyzes the complexity and potential immunological uniqueness of protein domains based on their primary sequence. Additionally, it can identify organized and disorganized regions of the protein, which is useful for evolutionary studies.
Hydropathy of protein domains
Stability & Mutability of protein domains
EpiQuest-M
The program assesses the likelihood of spontaneous mutations in different regions in the absence of selective pressure, based on the probabilities of individual amino acid replacements. It enables users to identify regions most susceptible to stability in rapidly replicating and evolving sequences that accumulate point mutations, such as viral proteins.
Statistics for Protein Sequence
Protein Charge and pI point
InCharge
A utility program designed to predict the pI (isoelectric) point of a peptide or protein, along with its charge at various pH levels. Originally developed for peptide analysis, it has undergone extensive testing with protein sequences as well. InCharge has demonstrated superior performance compared to its analogues and competitors when tested on a set of proteins with experimentally determined pI points. This holds true across a wide range of protein sizes, from 5 to 200 kD.
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