Appeal No. 2004-2139
Application No. 09/181,601
catalytic triads with well-conserved conformations to form the basis for calculating a final
3-D template known as the functional template. Id. Wallace still further discloses that
the functional 3-D template was employed to identify other Ser-His-Asp catalytic triads
in the PDB as opposed to noncatalytic triads. Id., p. 1009, col. 2. Wallace still further
discloses correlating the biochemical function of the newly-identified triads with the
biochemical function of the functional consensus Ser-His-Asp template. Id.,
Figure 5.
In view of these results, Wallace concludes that “[a]s the number of known
protein structures increases, so the need for a 3D equivalent of PROSITE grows with it-
especially for identifying likely functions of proteins whose biological role is unknown
and, equally usefully, for locating the functional regions and residues involved.”
Wallace, p. 1001, cols. 1-2.
2. Holm discloses that recent growth in the information of 3-D protein
structures using X-ray crystallography and NMR has resulted in making structure-
structure comparisons in order to elucidate evolutionary relationships between proteins.
Holm, p. 478, cols. 2-3. Holmes further discloses that to determine whether a particular
structure is unique or similar to known proteins, those skilled in the art can turn to the
European Molecular Biology Laboratory which is providing Internet access to the DALI
method of protein structure comparison which includes “a database of pre-calculated
structural neighbours for all public structures.” Id. Holm still further discloses that the
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