Appeal No. 2004-2139
Application No. 09/181,601
alignment and functional determination of a protein with the NMR and X-ray
crystallography methods and the 3-D database search information taught by Holm to
determine whether a protein structure is unique or similar to other known proteins by
comparison with structures in the Protein Data Bank. That is, given the teachings of
Wallace and Holm, it would have been obvious to one of ordinary skill in the art to
determine the biochemical function of an unknown 3-D protein structure by comparing
with known 3-D protein structures. Answer, p. 6. The examiner argues that it would
have been further obvious to said persons to use domains of 50-300 amino acids
because Holm teaches screening domains in this size range. Id. The examiner argues
that it would have been still further obvious to combine the methods of Wallace and
Holm with the teachings of Farber to predict coding regions in an unknown DNA
sequence “in order to maximize the usable databases to identify homologous proteins
and thereby determine the function of unknown proteins.” Id., p. 7.
In response, the appellants contend that the art does not suggest two of the
limitations set forth in representative claim 1; viz., the use of putative polypeptide
domains of 50 to 300 amino acids and the prestep of parsing the target polypeptide.
Brief, p. 14. The appellants contend that Wallace teaches neither of these limitations
and that even though Holm taught one comparison of 195 amino acid domains, it did
not teach that size is an important factor. Id. Thus, the appellants contend that the
applied prior art does not teach or suggest the claimed method. Id., p. 15. According to
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