Mimotope-based B-cell epitope detection software tools | Immune system data analysis
Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years.
Predicts epitopes using combinatorial phage-display libraries. PepSurf maps each of the affinity selected peptides onto the surface of antigen. It aims to find interacting interfaces by only considering solvent-exposed residues. This tool is statistically robust and can easily import features of general alignment problems such as gap penalties, different substitution matrices, profile versus sequence alignment, and so forth.
Discovers the genuine epitope on the surface of antigen. Mapitope is based on the original notion that the panel of peptides derived from a random peptide library collectively represents the epitope of monoclonal antibody (mAb) which they bind. It accepts as input a set of peptides obtained from screening phage display peptide-libraries and the 3D structure of the antigen.
Maps a conformational epitope on the antigen protein surface from phage display sequences without manual intervention. EpiSearch is based on a patch analysis that identifies spatial contiguous clusters of residues on the surface of antigen with similar physical-chemical properties as found in the phage display sequences. It provides feature to vary the cut off value for solvent accessible surface area of amino acids and the patch size.
Allows users to make epitope prediction using affinity-selected peptides derived from phage display experiments thanks to a graph mapping method. MimoPros includes a searching algorithm operated on a series of overlapping patches on the surface of a protein. It generates graphs by using an adaptable distance threshold (ADT) regulated by compactness factor (CF) which includes a certain number of vertices.
Allows phage display based epitope mapping. MIMOX can be used to align a set of mimotopes and derive a consensus sequence. It assists molecular biologists to identify the native epitope of an antibody based on the antigen structure and a set of mimotope sequences they get through phage display technology. This tool is able to find all the residue neighbour pairs between consecutive candidate residue arrays in the array.
A method for B-cell epitope prediction based on mimotope analysis. As a publicly available tool, Pep-3D-Search can be utilized and conveniently evaluated, and it can also be used to complement other existing tools.
Provides a 3D epitopic region prediction from the information content of mimotope peptide sequences. MIMOP can predict continuous as well as discontinuous epitopes. It permits to analyze a set of mimotope sequences and guide researchers in the identification of mimicked epitopic region. This tool is adaptable to any dataset or to specific knowledge of the antigen.