SEPPA

SEPPA predicts spatial epitopes on protein antigens to identify conformational epitope regions recognized by antibodies.

Key Features:

• Unit Patch of Residue Triangle: Introduces the "unit patch of residue triangle" to represent local three-dimensional arrangements of surface residues.
• Clustering Coefficient: Incorporates a clustering coefficient that quantifies the spatial compactness of surface residues to identify likely epitope regions.
• Performance Metrics: Validated on independent testing datasets with an average Area Under the Curve (AUC) value over 0.742 and a successful pick-up rate of 96.64%.
• Comparison with Other Methods: Demonstrates improved performance relative to CEP, DiscoTope, and BEpro in benchmark comparisons.
• Threshold Scores for Confidence Levels: Provides threshold scores corresponding to specific levels of accuracy, sensitivity, and specificity.

Scientific Applications:

• Vaccine Design: Assists identification of antigen surface regions for vaccine antigen selection.
• Antibody Development: Aids identification of target epitopes for antibody engineering and selection.
• Immunotherapy: Supports identification of therapeutic targets and characterization of immune responses at the molecular level.
• Epitope Mapping of Discontinuous Regions: Enables analysis of conformational/discontinuous epitope regions involved in complex protein–antibody interactions.

Methodology:

Defines a "unit patch of residue triangle" to describe local surface residue arrangements, computes a clustering coefficient to measure spatial compactness, applies threshold scores for confidence calibration, and was validated on independent testing datasets and benchmarked against CEP, DiscoTope, and BEpro.