AbEMap

AbEMap predicts antibody epitopes by performing protein–protein docking and analysis of antibody–antigen interactions to identify antigen residues likely forming epitopes.

Key Features:

• ClusPro and ClusPro-TBM docking: Uses ClusPro and its template-based modeling extension ClusPro-TBM for protein–protein docking of antibody–antigen complexes.
• X-ray Structure Mode: Utilizes experimentally determined X-ray crystallography structures as input for precise docking.
• Computational/Predicted Model Mode: Accepts computational or predicted antibody models as input for docking and interaction analysis.
• Sequence-Based Mode: Operates from the antibody amino acid sequence when structural data is unavailable, enabling sequence-driven epitope prediction.
• AlphaFold2 (AF2) integration: Supports the use of AlphaFold2 (AF2)-generated antibody models as docking input.
• Epitope likelihood scoring: Provides a per-residue likelihood score indicating the probability that each antigen residue is part of an epitope.

Scientific Applications:

• Epitope mapping: Predicts which antigen residues are likely components of antibody epitopes to map antibody binding sites.
• Vaccine development: Identifies candidate epitope residues to inform vaccine antigen design.
• Therapeutic antibody design and immunological studies: Supports selection and optimization of antibody targets and analysis of antibody–antigen interactions in immunology research.

Methodology:

Performs protein–protein docking using ClusPro and ClusPro-TBM, accepts AF2-generated models, and applies input-mode-specific strategies: X-ray structures use spatial coordinates for docking, predicted models use structural predictions for docking, sequence-based mode employs sequence alignment and prediction algorithms, and the server reports per-residue epitope likelihood scores.