Appeal 2007-0537
Application 10/102,902
provide the best match to the query triplet of interest.” (Cornilescu 289
(Abstract).)
10. Cornilescu uses this information to identify protein backbone
angle restraints through sequence homology and similar patterns of
secondary chemical shifts for triplets of adjacent residues (i.e., shifts related
to secondary, 3-dimensional structure). (E.g, Cornilescu 290 (“if a string of
adjacent amino acids shows high similarity in secondary chemical shifts
with a string of amino acids in a database, the central residues in the two
strings are likely to have similar backbone torsion angles”); see also Answer
16.).
11. Cornilescu’s “computer program TALOS was developed to
search for strings of residues with chemical shift and residue type homology.
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 was optimized empirically.” (Cornilescu 289 (Abstract), quoted in
Answer 7.)
12. Cornilescu also teaches an alignment step. (Cornilescu 289
(Abstract) (“Tests carried out for proteins of known structure indicate that
the root-mean-square difference (rmsd) between the output of TALOS and
the X-ray derived backbone angles is about 15 degrees.”), quoted in Answer
7. See also Cornilescu 293 (Figure 1).)
13. Cornilescu would have suggested to the skilled artisan the use of
such data to identify homologous proteins. (Cornilescu 289 (Abstract); see
also 293 (Fig. 1).)
7
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