Appeal 2007-0537
Application 10/102,902
14. Based on our definition of “fragment pair,” Cornilescu’s amino
acid residues qualify as a “series of molecular fragment pairs, where each
amino acid is separated by a peptide dihedral.” (Answer 7.)
15. Cornilescu searches “a database for triplets of adjacent residues
with secondary chemical shifts and sequence similarity which provide the
best match to the query triplet of interest." (Cornilescu 289 (Abstract); see
also Answer 16.)
16. Thus, Cornilescu identifies secondary chemical shifts and
sequence similarity between triplets of adjacent residues and the query
triplet of interest, i.e., “features of a candidate molecule fragment pair which
correspond to features of a query molecule fragment pair.” (See claim 1.)
17. Cornilescu’s “database contains . . . chemical shifts for 20
proteins for which a high resolution X-ray structure is available” and is
searched “for strings of residues with chemical shift and residue type
homology.” (Cornilescu 289 (Abstract); see also Answer 6-7.)
18. Cornilescu optimizes empirically the “relative importance of the
weighting factors attached to the secondary chemical shifts of the five types
of resonances relative to that of sequence similarity." (Id. (citing Table 2 for
a listing of such weighting factors, “by which the chemical shift data are
scaled”); see also Answer 7, 19-20.) Thus, Cornilescu uses “context-
adaptive scaling” to give weight to the chemical environment.
19. Gilhuijs, like Cornilescu, relates to “studies of magnetic
resonance of biological materials” and discloses standard computer
hardware, including means to “display and input results” (Answer 11 (citing
Giluijs’s Fig. 3).) Thus Gilhuijs’s teachings would have been relevant to
further utilizing Cornilescu’s method on a computer.
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