PepMapper

PepMapper predicts B-cell epitope locations on antigens by mapping mimotopes derived from phage display experiments to antigen surface regions.

Key Features:

• Mimotope-Based Mapping: Leverages structural and functional similarities between mimotopes (peptides from phage display) and native B-cell epitopes to predict epitope locations on antigens.
• Advanced Algorithm: Implements a search algorithm that integrates dynamic programming (DP) and branch and bound (BB) optimization to operate on overlapping protein surface patches transformed into graphs using an adaptable distance threshold (ADT) regulated by a compactness factor (CF).
• Performance Metrics: Demonstrated superior sensitivity, precision, and Matthews correlation coefficient (MCC) compared to Pep-3D-Search and PepSurf across 18 test cases.
• Efficiency: Achieves substantially faster execution than Pep-3D-Search and PepSurf.

Scientific Applications:

• Vaccine design: Identifying precise epitope locations on antigens to inform antigen selection and epitope-focused vaccine design.
• Immunological research: Aiding study of antigen–antibody interactions and B-cell epitope characterization.
• Diagnostic development: Supporting development of diagnostic reagents by locating antigenic regions targeted by antibodies.

Methodology:

Maps mimotopes to antigens using overlapping protein surface patches, converts patches to graphs via an adaptable distance threshold (ADT) regulated by a compactness factor (CF), and searches the graphs with an algorithm combining dynamic programming (DP) and branch and bound (BB) optimization.