Protein structure analysis

Details Protein structure analysis Protein structure analysis

2011-08-30

2011-08-30

Borin, Michael (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S027000

Reexamination Certificate

active

08010297

ABSTRACT:
Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

REFERENCES:
patent: 7343246 (2008-03-01), Silverman
Eisenberg et al., “Hydrophobic Moments and Protein Structure,” Faraday Symp. Chem. Soc., 17:109-120 (1982).
Felts et al., “Distinguishing Native Conformations of Proteins from Decoys with an Effective Free Energy Estimator Based on the OPLS All-Atom Force Field and the Surface Generalized Born Solvent Model,” Proteins: Structure, Function, and Genetics, 48:404-422 (2002).
Silverman, D.B., “Hydrophobic Moments of Protein Structures: Spatially Profiling the Distribution,” Columbia University, Proc. Nat'l Acad. Sci. U.S.A. 98, 4996-5001 (2001).
Silverman, D.B., “A Two-Component Nucleation Model of Protein Hydrophobicity,” J. Theor. Biol., 216:139-146 (2002).
Zhou et al., “Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling,” Proceedings of Pacific Symposium on Biocomputing 2002, Eds. R.B. Altman, A.K. Dunker, L. Hunter, K. Lauderdale and T.E. Klein, 673-684, World Scientific, Singapore (2002).

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