Appeal No. 2004-2139
Application No. 09/181,601
DALI server is capable of performing a database search with a new structure against all
structures in the PDB. Id., col. 3. Holm still further discloses that co-ordinates of new
structures can be submitted electronically to the PDB and “a list of all structural
neighbors of the query structure in protein fold space and optimal structural alignment
with each neighbour is returned.” Id.
In addition, Holm lists several web servers “related to 3-D protein structure”
which include, inter alia, the DALI server- a database search by comparison of 3-D
structures, CATH- which provides a structural classification of proteins, PDB- which
retrieves 3-D co-ordinates. Id., p. 480, Table II. Holm exemplifies a comparison
between the 3-D structure of urease and adenosine deaminase. Id., p. 479, Figure 1.
3. Farber discloses using computational procedures (algorithms) to analyze
raw nucleotide sequence data such as that provided by the Human Genome project, to
predict coding regions within DNA. Farber, pp. 471-472 and p. 478, col. 1.
The examiner argues that in view of the teachings of Wallace with respect to the
use of databases of 3-D templates to identify the functions of new protein structures as
they are elucidated (the abstract), and the teachings of Holm with respect to the use of
(i) NMR and X-ray crystallography to elucidate new protein structures; and (ii) the DALI
server to perform a search which compares a new protein structure with known protein
structures in the Protein Data Base, it would have been obvious to one of ordinary skill
in the art to combine the teachings of Wallace with respect to the 3-D structural
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