The EFI has five Scientific Cores for: 1) directing target selection and devising strategies for functional assignment based on sequence relationships and genome context; 2) cloning, expression, and purification of targets; 3) experimental determination of structures of targets; 4) homology modeling and in silico docking of ligand libraries for targets; and 5) microbiological and metabolomic characterization of the in vivo roles of targets. Additionally, a sixth Data and Dissemination Core is responsible for development and maintenance of appropriate resources for deposition of EFI data (e.g. EFI-DB) and mechanisms for disseminating EFI tools and strategies.
The functional predictions are tested by Bridging Projects that focus on functionally diverse superfamilies. While each of these superfamilies share conserved partial reactions, the identities of the substrates/products are not conserved and functional assignment cannot be accomplished by transfer of prior annotations based only on sequence or structural similarity.