Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-09-27
2005-09-27
Horlick, Kenneth R. (Department: 1637)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S027000
Reexamination Certificate
active
06950754
ABSTRACT:
The present invention relates to apparatus and methods for quantitative protein design and optimization.
REFERENCES:
patent: 4939666 (1990-07-01), Hardman
patent: 5241470 (1993-08-01), Lee et al.
patent: 5527681 (1996-06-01), Holmes
patent: 6188965 (2001-02-01), Mayo et al.
patent: 6269312 (2001-07-01), Mayo et al.
patent: WO 95/22625 (1995-08-01), None
patent: WO 98/32845 (1998-07-01), None
patent: WO 00/23564 (2000-04-01), None
patent: WO 00/68396 (2000-11-01), None
patent: WO 01/59066 (2001-08-01), None
patent: WO 01/59066 (2001-08-01), None
U.S. Appl. No. 09/837,886.
Gallop et al., “Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries,” Journal of Medicinal Chemistry vol. 37, No. 9, (Apr. 29, 1994), 1233-1251.
Lam, Kit S., “Application of Combinatorial Library Methods in Cancer Research and Drug Discovery,” Anti-Cancer Drug Design (1997), 12, 145-167.
Wilson et al., “Computational Method for the Design of Enzymes with Altered Substrate Specificity”, J. Mol. Biol. (1991) 220, 495-506.
Brenner and Berry, A., et al., “A quantitative methodology for the de novo design of proteins”, Protein Sci. 3:1871-1882 (Oct. 1994).
Borman, “Proteins to Order,” Chemical and Engineering Newsletter (C&EN) Oct. 6, 1997, 9-10 (1997).
Bowie, J.U., et al., “Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substituions”, Science vol. 247:1306-1310 (Mar. 1990).
Bowie, J.U., et al., “A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure”, Science vol. 253:164-170 (Jul. 1991).
Brooks et al., “CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations,” J. of Computational Chemistry, 4(2):187-217 (1983).
Connolly, M.L., “Solvent-Accessible Surfaces of Proteins and Nucleic Acids”, Science vol. 221(4612):709-713 (Aug. 1983).
Cornell et al., “A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules,” J. Am. Chem. Soc., 117:5179-5197 (1995).
Dahiyat, B.I., et al., “Automated design of the surface positions of protein helices”, Protein Science 6:1333-1337 (Jun. 1997).
Dahiyat et al., “Protein design automation,” Caltech Biology Annual Report, 172 (1995).
Dahiyat, B.I., et al., “Proteins from Scratch”, press digest email by Science (Sep. 26, 1997).
Dahiyat et al., “Protein Design Automation,” Meeting Abstract; Protein Science vol. 4, Suppl. 2, 83 (1995).
Dahiyat et al., “Protein design Automation,” Poster Sessions, Protein Science vol. 5, Suppl. 1, 22-23 (1996).
Dahiyat et al., “De Novo Protein Design: Fully Automated Sequence Selection,” Science, 278:82-87 (1997).
Dahiyat et al., “Probing the Role of Specificity in Protein Design,” Caltech Biology Annual Report, 160-161 (1996).
Dahiyat et al., “Protein Design Automation,” 1996, Protein Science, vol. 5, pp. 895-903, Nov. 30, 1999.
Dahiyat, B.I., et al., “First fully automatic design of a protein achieved by Caltech scientists”, new press release (Oct. 1997).
Dalal, S., et al., “Protein alchemy: Changing .beta.-sheet into .alpha.-helix”, Nature Struc. Biol. vol. 4(7):548-552 (Jul. 1997).
DeGrado, W., “Proteins from Scratch,” Science, 278:80-81 (1997).
Desjarlais, J.R., et al., “De novo design of the hydrophobic cores of proteins”, Protein Science 4:2006-2018 (1995).
Desjarlais et al., “New strategies in protein design,” Current Opinion in Biotechnology: 460-466 (1995).
Desmet, J., et al., “The ‘Dead End Elimination’ Theorem: A New Approach to the Side Chain Packing Protein”, from “The Protein Folding Problem and Tertiary Structure Prediction” Ch. 10:1-49 (1994).
Desmet, J., et al., “The dead-end elimination theorem and its use in protein side-chain positioning”, Nature vol. 356:539-542 (Apr. 1992).
Desmet et al., “Theoretical and Algorithmical Optimization of the Dead-End Elimination Theorem,” Proceedings of the Pacific Symposium on Biocomputing '97, 122-133 (1997).
Dunbrack Jr., R.L., et al., “Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains”, Struc. Biol. vol. 1(5):334-340 (May 1994).
Eisenberg, D., et al., “Solvation energy in protein folding and binding”, Nature vol. 319:199-203 (Jan. 1986).
Goldstein, R.F., “Efficient Rotamer Elimination Applied to Protein Side-Chains and Related Spin Glasses”, Biophys. Jour. vol. 66:1335-1340 (May 1994).
Gordon et al. “Energy functions for protein design,” Curr. Opinion in Struct. Biol., 9:509-513 (1999).
Harbury et al., “Repacking protein cores with backbone freedom: Structure prediction for coiled coils,” Proc. Natl. Acad. Sci. USA, 92:8408-8412 (1995).
Harbury et al., “High-Resolution Protein Design with Backbone Freedom,” Science, 282:1462-1467 (1998).
Hellinga, H.W., et al., “Construction of New Ligand Binding Site in Proteins of Known Structure”, J. Mol. Biol. 222:763-785 (1991).
Hellinga, H.W., “Rational protein design: Combining theory and experiment”, Proc. Natl. Acad. Sci, USA vol. 94:10015-10017 (Sep. 1997).
Hellinga, H.W., et al., “Optimal sequence selection in proteins of known structure by simulated evolution”, Proc. Natl. Acad. Sci., USA vol. 91:5803-5807 (Jun. 1994).
Holmes, “First-ever designer protein fits like a glove,” New Scientist, IPC Magazines Limited, Oct. 11, 1997 (1997).
Hurley et al., “Design and Structural Analysis of Alternative Hydrophobic Core Packing Arrangements in Bacteriophage T4 Lysozyme,” J. Mol. Biol., 224:1143-1159(1992).
Jones, D.T., “De novo protein design using pairwise potentials and a genetic algorithm”, Protein Science 3:567-574 (1994).
Koehl et al., “De Novo Protein Design I. In Search of Stability and Specificity,” J. Mol. Biol., 293:1161-1181 (1999).
Kono et al., “Energy Minimization Method Using Automata Network for Sequence and Side-Chain Conformation Prediction from Given Backbone Geometry,” Proteins: Structure, Function, and Genetics, 19:244-255 (1994).
Kortemme et al., “Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein,” Science, 281:253-256 (1988).
Lasters et al., “Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains,” 1995, Protein Engineering, vol. 8, No. 8, pp. 815-822.
Lasters, I., et al , “Dead-End Based Modeling Tools to Explore the Sequence Space That is Compatible with a Given Scaffold”, Jour. of Protein Chem. vol. 16(5):449-452 (Jul. 1997).
Lazar et al., “De novo design of the hydrophobic core of ubiquitin,” Protein Science 6:1167-1178 (1997).
Lee et al, “Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core,” Nature, 352:448-451 (1991).
Lim et al., “The crystal structure of a mutant protein with altered but improved hydrophobic core packing,” Proc Natl Acad Sci U S A. Jan 4, 1994;91(1):423-7.
Mayo et al., “Dreiding: A Generic Force Field for Molecular Simulations,” J. Phys. Chem., 94:8897-8909 (1990).
Minor Jr., D.L., “Measurement of the .beta.-sheet-forming propensities of amino acids”, Nature vol. 367:660-663 (Feb. 1994).
Munoz, V., et al., “Helix design, prediction and stability”, Curr. Opin. in Biotech. 6:382-386 (Aug. 1995).
Munoz, V., et al., “Intrinsic Secondary Structure Propensities of the Amino Acids, Using Statistical phi-psi Matrices: Comparison with Experimental Scales”, Proteins 20:301-311 (1994).
Munoz, V., et al., “Analysis of the effect of local intera
Dahiyat Bassil I.
Gordon D. Benjamin
Mayo Stephen L.
Street Arthur
Su Yaoying
Dorsey & Whitney LLP
Horlick Kenneth R.
Kim Young J.
Silva Robin M.
The California Institute of Technology
LandOfFree
Apparatus and method for automated protein design does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Apparatus and method for automated protein design, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Apparatus and method for automated protein design will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3379243