Appeal 2007-0537
Application 10/102,902
“descriptors.” These are the specific terms Appellants argue are not taught
or suggested by the cited prior art. (App. Br. 12-18; Reply Br. 1-4.)
The Examiner primarily relies upon Cornilescu. Cornilescu describes
using a computer system and program (TALOS) to compare secondary
chemical shift and sequence data for triplets of amino acid residues of
unknown proteins with such data for triplets of known proteins. TALOS
was developed to search their database for “strings of residues with chemical
shift and residue type homology” (Cornilescu 289 (abstract)). Cornilescu’s
system was designed based on the recognition that “[c]hemical shifts of
backbone atoms in proteins are exquisitely sensitive to local conformation,
and homologous proteins show quite similar patterns of secondary chemical
shifts.” (Id.)
The Examiner equates “triplets of amino acid residues” with
“fragment pairs” (Answer 7, 16-18), “chemical shifts” with “features of a
fragment pair” or “descriptors” (Answer 17, 19, 20), and “k-values scaling”
of the chemical shifts with “context-adaptive scaling” (Answer 19-20).
Thus, the key issue before us is, do the disputed claim terms
“fragment pair,” “features” of a fragment pair (or “descriptors”), and
“context-adaptive scaling” in claim 1 encompass Cornilescu’s “triplets of
amino acid residues,” “chemical shifts,” and “k-values scaling,”
respectively?
Findings of Fact
Claim Interpretation
1. The Specification defines “fragment pair” as follows: “A fragment
pair consists of two neighboring fragments connected by a rotatable bond at
a specific dihedral angle.” (Spec. 21; see also Answer 7.) “By this
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