EpiBuilder

EpiBuilder assembles and analyzes B-cell epitopes to characterize epitope topology and enable proteome-wide epitope discovery for immunological and vaccine research.

Key Features:

• Epitope Assembly: Assembles epitopes from input predictions such as BepiPred-2.0.
• Epitope Classification and Proteome Search: Classifies epitopes and supports searching within proteomes for proteome-wide analysis.
• Chou & Fasman Beta-turn Prediction: Applies Chou & Fasman beta-turn prediction to epitope regions.
• Emini Surface Accessibility Prediction: Applies Emini surface accessibility prediction to assess residue exposure.
• Karplus and Schulz Flexibility Prediction: Applies Karplus and Schulz flexibility prediction to evaluate local peptide mobility.
• Kolaskar and Tongaonkar Antigenicity Assessment: Applies Kolaskar and Tongaonkar antigenicity assessment to estimate probable antigenic regions.
• Parker Hydrophilicity Prediction: Applies Parker hydrophilicity prediction to assess hydrophilic character of epitopes.
• N-glycosylation Domain Identification: Identifies N-glycosylation domains within epitope sequences.
• Hydropathy Analysis: Performs hydropathy analysis on epitope sequences.
• Epitope Topology Generation: Combines predictive features to generate a topology profile for each epitope.
• Sequence Search and BLASTP: Searches epitope sequences across FASTA files and uses BLASTP to identify sequence variations across proteomes.

Scientific Applications:

• Proteome-wide epitope discovery: Generates epitope datasets from organisms such as Trypanosoma brucei gambiense, Clostridioides difficile, and SARS-CoV-2 for comparative analyses.
• Vaccine candidate identification: Supports identification and characterization of B-cell epitope candidates for vaccine and immunological research.
• Comparative epitope variation analysis: Enables detection of sequence variation in epitopes across proteomes using FASTA searches and BLASTP.

Methodology:

Accepts BepiPred-2.0 inputs and applies Chou & Fasman, Emini, Karplus & Schulz, Kolaskar & Tongaonkar, and Parker algorithms plus N-glycosylation and hydropathy analyses; performs sequence searches across FASTA files and BLASTP-based variation detection and generates per-epitope topology profiles.