To determine the function of an orphan gene we examine the 3-D structure of the protein this gene is expected to encode; such a protein is termed as hypothetical protein. This 3D structure is compared with the protein structures stored in databases. This basis for approach is the fact that the structures of proteins are more conserved than are their primary structures. This is because protein functions depend on the 3D structure rather than the primary structure of protein.
It reveals the general function of protein. A higher resolution in the characterization may be possible by matching the shape of the cleft to a library of small molecular shapes, using drug design software like DOCK and HOOK. These programmes identify potential ligands to binding sites on protein surfaces. Surfaces scanning would also allow recognition of domains most likely involved in interaction with other proteins.
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