EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes

Abstract

Epitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as ABCPred, SVMTrip, EpiDope, and EpitopeVec; a well-known BCE predictor is BepiPred-2.0. However, despite the prediction, there are several essential steps, such as epitope assembly, evaluation, and searching for epitopes in other proteomes. Here, we present EpiBuilder ( https://epibuilder.sourceforge.io ), a user friendly software that assists in epitope assembly, classifying and searching using input results of BepiPred-2.0. EpiBuilder generates several output results from these data and supports a proteome-wide processing approach. In addition, this software provides the following features: Chou & Fasman beta-turn prediction, Emini surface accessibility prediction, Karplus and Schulz flexibility prediction, Kolaskar and Tongaonkar antigenicity, Parker hydrophilicity prediction, N-glycosylation domains, and hydropathy. These information generate a unique topology for each epitope, visually demonstrating its characteristics. The software can search the entire epitope sequence in various FASTA files, and it allows to use BLASTP to identify epitopes that eventually have sequence variations. As an EpiBuilder application, we developed a epitope dataset from the protozoan Trypanosoma brucei gambiense, the gram-positive bacterium Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).