Appeal No. 2002-0796 Page 9
Application No. 09/110,994
a protein-protein interaction, and in fact, teaches away from the present
invention. See id. at 5-6.
The above arguments are not found to be convincing. Although Petrenko
may be drawn to identifying phage with certain characteristics drawn from their
“surface landscape,” claim 1 does not exclude the use of such a phage library.
All that is required by claim 1 is that the library yield a peptide sequence, and the
library used in the method described by Petrenko does lead to the determination
of a consensus peptide sequence, EPFP. The rejection acknowledges that
Petrenko does not describe the step of determining the identity of a protein upon
any putative consensus sequence they determined using the screening process,
relying on Ivanenkov and Sparks to make up that deficiency. And as already
noted, one of ordinary skill would have been motivated to combine the teachings
of Petrenko, Ivanenkov and Sparks in order to determine known proteins that
have sequences that may be capable of binding to small ligands, such as dioxin,
in order to determine potential biological targets and potential unexpected
sources of interaction and/or toxicities. With respect to the ConA example of
Petrenko, the example demonstrates that using the same selection procedure as
used for dioxin, the reference was able to isolate a sequence that binds to a
protein, as well as a sequence that binds to a small ligand such as dioxin,
demonstrating that the screening is suitable for the determination of any specific
binding interaction, be it binding to a protein or binding to a small ligand.
Appellants’ arguments pointing out the problems associated with using an
octapeptide library for screening, and that they used a P3 library in their
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