Appeal No. 2004-2139
Application No. 09/181,601
1. A high-throughput method for determining the biochemical function of a
protein or polypeptide domain of unknown three dimensional structure and function
comprising:
(A) parsing a target polynucleotide into at least one putative polypeptide
domain;
(B) identifying a putative polypeptide domain consisting of 50 to 300 amino
acids that properly folds into a stable polypeptide domain consisting of 50 to 300 amino
acids;
(C) determining three dimensional structure of the stable polypeptide domain;
(D) comparing the determined three dimensional structure of the stable
polypeptide domain to known three-dimensional structures in a protein data bank,
wherein said comparison identifies known structures within said protein data bank that
are homologous to the determined three dimensional structure; and
(E) correlating a biochemical function corresponding to the identified
homologous structure to a biochemical function for the stable polypeptide domain.
The references relied upon by the examiner are:
Friedrichs et al. (Friedrichs), “An Automated Procedure for the Assignment of Protein
1HN, 15N, 13C", 1H", 13Cb and 1H$ Resonances*,” J. Biomolecular NMR, Vol. 4, pp. 703-
726 (1994).
Farber et al. (Farber), “Determination of Eukaryotic Protein Coding Regions Using
Neural Networks and Information Theory,” J. Mol. Biol., Vol. 226, pp. 471-479 (1992).
Holm et al. (Holm), “Dali: A Network Tool for Protein Structure Comparison,” Trends
Biotechnol. Vol. 85, pp. 478-480 (1995).
Wallace et al. (Wallace), “Derivation of 3D Coordinate Templates for Searching
Structural Databases: Application to Ser-His-Asp Catalytic Triads in the Serine
Proteinases and Lipases,” Protein Science, Vol. 5, pp. 1001-1013 (June 1996).
Bagby et al. (Bagby), “The Button Test: A Small Scale Method Using Microdialysis Cells
for Assessing Protein Solubility at Concentrations Suitable for NMR,” J. Biomolecular
NMR, Vol. 10, pp. 279-282 (1997).
The claims stand rejected as follows:
2
Page: Previous 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Next
Last modified: November 3, 2007