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AssigneeThe Scripps Research Institute
InventorsJeffrey Skolnick, Jacquelyn S. Fetrow
Estimating the term…
The present invention concerns methods and systems for predicting the biological function(s) of proteins. The invention is based on the development of functional site descriptors for discrete protein biological functions. Functional site descriptors are geometric representations of protein functional sites in three-dimensional space, and can also include additional parameters, for example, conformational information. Following their development, one or more functional site descriptors (for one or more different biological functions) are used to probe protein structures to determine if such structures contain the functional sites described by the corresponding functional site descriptors. If so, the protein(s) containing the functional site(s) are predicted to have the corresponding biological function(s). In preferred embodiments, a library of functional site descriptors is used to probe inexact protein structures derived by computational methods from amino acid sequence information to predict the biological function(s) of such sequences and of the gene(s) encoding the same.
A functional site descriptor that defines a spatial configuration for a functional site of a protein, which functional site corresponds to a biological function other than a divalent metal ion binding site, for application to an inexact, three dimensional structural model of a protein to determine whether the protein possesses the biological function corresponding to the functional site defined by the functional site descriptor, the functional site descriptor comprising a set of geometric constraints for one or more atoms in each of two or more amino acid residues comprising a functional site of a protein other than a divalent metal ion binding site, wherein at least one of said two or more amino acid residues is identified as a particular amino acid residue or set of amino acid residues, wherein said one or more atoms is selected from the group consisting of amide nitrogens, α-carbons, carbonyl carbons, and carbonyl oxygens within a polypeptide backbone, β-carbons of amino acid residues, and pseudoatoms, and wherein at least one of said one or more atoms is an amide nitrogen, an α-carbon, a β-carbon, or a carbonyl oxygen within a polypeptide backbone.
Method of identifying a protein as having a particular biological function, the method comprising:
Method of making a functional site descriptor that defines a spatial configuration for a functional site of a protein, which functional site corresponds to a biological function other than a divalent metal ion binding site, for application to an inexact, three dimensional structural model of a protein to determine whether the protein possesses the biological function corresponding to the functional site defined by the functional site descriptor, the method comprising developing a set of geometric constraints for one or more atoms in each of two or more amino acid residues comprising a functional site of a protein other than a divalent metal ion binding site, wherein at least one of said two or more amino acid residues is identified as a particular amino acid residue or set of amino acid residues, wherein said one or more atoms is selected from the group consisting of amide nitrogens, α-carbons, carbonyl carbons, and carbonyl oxygens within a polypeptide backbone, β-carbons of amino acid residues, and pseudoatoms, and wherein at least one of said one or more atoms is an amide nitrogen, an α-carbon, a β-carbon, or a carbonyl oxygen within a polypeptide backbone.
A computer program product comprising a computer useable medium having computer program logic recorded thereon for creating a functional site descriptor for use in predicting a biological function of a protein, said computer program logic comprising computer program code logic configured to perform the operations of:
Dependencies are inferred from the claim text.