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).

Keywords: BepiPred-2.0; Galaxy; Immunoinformatics.

Figure 1.

Topology generated by EpiBuilder, the epitope is individually analyzed with visual presentation of its features, besides presenting the element All Matches, where the amino acid is above the cutoff point in all selected methods. The topology also presents the sites of N-glycosylation and also hydropathy.

Figure 2.

The complete EpiBuilder pipeline, indicating input files (BepiPred-2.0 files and proteomes for query) and the internal process such as input loading and processing of software scores, searching for N-glycosylation, assembling of the topology, and the searching in proteomes. After all these steps, the reports are generated in several files. IEDB indicates Immune Epitope Database; MW, molecular mass; IP, Isoleletric Point.

Figure 3.

EpiBuilder desktop main screen. From this screen, the user can configure the input file, threshold, the minimum and maximum size of epitopes, the additional features it intends to analyze, the proteomes for searching the epitopes, and the option to search proteomes by BLASTP.

Figure 4.

EpiBuilder main screen on galaxy platform. From this screen, the user can configure the input file, threshold, the minimum and maximum size of epitopes, the additional features it intends to analyze, the proteomes for searching the epitopes, and the option to search proteomes by BLASTP.

Figure 5.

Alignment of the spike proteins (S) of SARS-CoV-2, compared with the VoC variants where it is possible to analyze that there are mutations that impact amino acids present in identified areas epitopes, especially in the omicron variant. The alignment was performed using Clustal Omega with default parameter values. SARS-CoV-2 indicates severe acute respiratory syndrome coronavirus 2; VoC, variant of concern.