EPI-peptide designer

EPI-peptide designer predicts paratope residues and generates peptide ligand libraries by extracting interacting residues from antibody–antigen interfaces and converting 3D complexes into interface graphs to target specific epitopes.

Key Features:

• Interface Interacting Residue (I2R): Employs the Interface Interacting Residue (I2R) method to identify interacting residues within antibody–antigen interfaces via computed molecular interactions.
• Interface Graph Transformation: Aggregates interacting residues to transform 3D antibody–antigen structures into interface graphs representing molecular contacts.
• Paratope Prediction: Predicts paratope residues for specified epitopes from interface graphs.
• Peptide Library Generation: Generates targeted peptide ligand libraries based on predicted paratope–epitope interactions.
• Enhanced Binding Prediction: Improves binding prediction accuracy with an observed enrichment of 22% over randomly generated peptides.

Scientific Applications:

• Biosensors: Designing peptides that specifically bind target proteins for biosensor applications.
• Diagnostics: Creating diagnostic reagents that detect biomarkers via peptide–protein interactions.
• Therapeutics: Developing therapeutic peptide candidates that target specific epitopes identified from antibody–antigen interfaces.
• LiD1 validation: Applied to the LiD1 target protein, predicting 301 peptides with 65% experimental validation among tested peptides.

Methodology:

Uses the Interface Interacting Residue (I2R) method to identify interacting residues from computed molecular interactions, aggregates these into interface graphs, predicts paratope residues for epitopes, and generates targeted peptide ligand libraries.