Patent ID: 6631332
Filing Date: 2003-10-07
Classification: C07K,G01N,G16B

Abstract:
A method of identifying a protein as having a particular biological function, the method comprising:(a) applying a functional site descriptor that correlates with the particular biological function to a structure of a protein, wherein said functional site defines a functional site corresponding to a function of a protein or family of proteins, other than a divalent metal ion binding site, the functional site descriptor being defined using at least one atom from each of about fifteen or fewer amino acid residues used to define said functional site and comprising: (i) an amino acid residue identity constraint for each amino acid residue used to define said functional site, wherein said amino acid residue identity constraint for each amino acid residue is a single amino acid residue identity or two or more alternative amino acid residue identities; (ii) one or more geometric constraints for at least three different atoms, wherein at least three of said different atoms are in different amino acid residues of the protein used to define said functional site and at least one of said atoms is selected from the group consisting of a backbone amide nitrogen, an alpha-carbon, a backbone carbonyl carbon, a backbone carbonyl oxygen, and a pseudoatom comprised of two or more of a backbone amide nitrogen, an alpha-carbon, a backbone carbonyl carbon, and a backbone carbonyl oxygen; and, (iii) each geometric constraint is associated with a variance in order to provide a degree of relaxation for each said geometric constraint; and (b) identifying the protein as having the biological function if application of the functional site descriptor reveals that a portion of the structure of the protein matches the constraints of the functional site descriptor.