Identifying Similar Allergens and Potentially Cross-Reacting Areas Using Structural Database of Allergenic Proteins (SDAP) Tools and D-Graph.

Abstract

The Structural Database of Allergenic Proteins (SDAP) provides rapid search tools to identify similarities among allergens, their IgE epitopes, and to determine the potential allergenicity of any novel protein. Many labs have identified IgE-binding proteins and their antibody binding or T cell epitopes using dotspots or microarrays. This chapter describes how to determine the relationship of these proteins and peptides to known allergens using the tools implemented in SDAP. One can also search with these smaller peptide similarity search tool implemented in SDAP to find similar sequences with low property distance (PD) values in the over 1500 sequences of allergens. The sequences can be compared by mapping on the surface of the protein structures provided for nearly all the allergens in SDAP. Once the user has a unique list of similar sequences, they can be graphed in 2D according to interpeptide PD values calculated automatically by the D-graph program. This chapter provides a step-by-step description of how to do this, starting from a protein similar to the Ole e 1 (olive pollen) allergen family.