Appeal 2007-0537
Application 10/102,902
not unfair to applicants, because ‘before a patent is granted the claims are
readily amended as part of the examination process’ . . . .” In re Hyatt, 211
F.3d 1367, 1372, 54 USPQ2d 1664, 1667 (Fed. Cir. 2000) (internal citations
omitted).
Claim 1
Each of the disputed terms in claim 1, “fragment pair,” “features,”
“descriptor,” and “context-adaptive scaling” are taught or suggested by
Cornilescu. (See FFs 2-7, 9-11, 14-18, 28 & 29.) While we recognize
Cornilescu focuses on identifying similar backbone torsion angles between
amino acid residues rather than identifying molecules with similar
structures, Cornilescu’s teachings would have suggested to the skilled
artisan the use of such data to obtain homologous molecules. (See FFs 9-
13.)
Given the scope of the disputed terms, Cornilescu discloses or
suggests all of the limitations of claim 1, including the computer hardware
(exemplified by Gilhuijs). (FFs 1-19, 22-29.) More specifically, Cornilescu
discloses a database with data (1) “pertaining to at least one candidate
molecule” (chemical shift and sequence data for triplets of amino acid
residues for 20 fully characterized proteins) and (2) “pertaining to a query
molecule” (chemical shift and sequence data for a triplet of amino acid
residues for Cornilescu’s protein of unknown structure).
Using a computer program (TALOS), Cornilescu “identifies a
candidate molecule,” (one or more proteins of known structure) which is
“similar to said query molecule” (Cornilescu’s uncharacterized protein).
This is accomplished by: “identifying features of a candidate molecule
fragment pair” (chemical shifts and sequences for triplets of amino acid
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