Appeal No. 2004-2139
Application No. 09/181,601
throughput” method of determining the function of a protein and protein domains by
examining their three dimensional (3-D) structure.
It is well known that a protein’s tertiary structure is determined by its primary
(amino acid) sequence. Specification, p. 2. The tertiary structure or folding of the
protein results in one or more autonomous units known as domains. Id., p. 3.
Multidomain proteins in higher organisms are said to be encoded by genes containing
multiple exons. Id.
The specification discloses that several techniques were known in the art for
determining the three dimensional structure of a protein molecule such as X-ray
crystallography and Nuclear Magnetic Resonance (NMR). Specification, p. 3.
According to the specification, it was rare for prior investigators to determine the three
dimensional structure of a protein before its biochemical function was determined by
other methods. Id., p. 5. The present invention is said to differ from past research
methods because it provides a means of first determining the three dimensional
structure of a protein whose function is unknown and using this structure to determine
its function. Id.
The first step in the present method is said to involve the use of a computer
algorithm to identify (or parse) putative polypeptide domain-encoding regions of a
target polynucleotide. Specification, p. 7, lines 5-7 and lines 22-23; p. 10, lines 23-34.
The second step is said to involve identifying polypeptide domains of 50 to 300 amino
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