Protein design automation for protein libraries

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

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C702S027000, C706S045000, C706S046000

Reexamination Certificate

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09927790

ABSTRACT:
The invention relates to the use of protein design automation (P DA) to generate computationally prescreened secondary libraries of proteins, and to methods and compositions utilizing the libraries.

REFERENCES:
patent: 4939666 (1990-07-01), Hardman
patent: 5241470 (1993-08-01), Lee et al.
patent: 5265030 (1993-11-01), Skolnick et al.
patent: 5436850 (1995-07-01), Eisenberg et al.
patent: 5527681 (1996-06-01), Holmes
patent: 5878373 (1999-03-01), Cohen et al.
patent: 6188965 (2001-02-01), Mayo et al.
patent: 6269312 (2001-07-01), Mayo et al.
patent: 6403312 (2002-06-01), Dahiyat et al.
patent: 2002/0048772 (2002-04-01), Dahiyat et al.
patent: 2002/0090648 (2002-07-01), Dahiyat et al.
patent: 2004/0043429 (2004-03-01), Dahiyat et al.
patent: 2004/0043430 (2004-03-01), Dahiyat et al.
patent: 0549107 (1993-06-01), None
patent: 95/22625 (1995-08-01), None
patent: WO98/05765 (1998-02-01), None
patent: 98/32845 (1998-07-01), None
patent: WO98/32845 (1998-07-01), None
patent: 98/47089 (1998-10-01), None
patent: WO98/47089 (1998-10-01), None
patent: 00/23564 (2000-04-01), None
patent: WO 00/40715 (2000-07-01), None
patent: 00/68396 (2000-11-01), None
patent: WO 01/37147 (2001-05-01), None
patent: WO 01/39098 (2001-05-01), None
patent: WO 01/61344 (2001-08-01), None
patent: WO 03/006154 (2003-01-01), None
patent: WO94/16090 (2004-07-01), None
Shakhnovich, E. Folding and Design, 1998, 3, R45-R58.
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 Substitutions”, Science vol. 247:1306-1310 (Mar. 1990).
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 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., “Probing the Role of Specificity in Protein Design,” Caltech Biology Annual Report, 160-161 (1996).
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 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 Elmination 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., “High-Resolution Protein Design with Backbone Freedom,” Science, 282:1462-1467 (1998).
Hellinga, H.W., “Rational protein design: Combining theory and experiment”, Proc. Natl. Acad. Sci, USA vol. 94:10015-10017 (Sep. 1997).
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).
Koehl et al., “De Novo Protein Design. I. In Search of Stability and Specificity,” J. Mol. Biol., 293:1161-1181 (1999).
Kortemme et al., “Design of a 20-Amino Acid, Three-Strandedβ-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 interactions on protein stability”, Folding & Design 1(3):167-178 (Apr. 1996).
Pabo, C., “Designing proteins and peptides”, Nature vol. 301:200 (Jan. 1983).
Padmanabhan, S., et al., “Relative helix-forming tendencies of nonpolar amino acids”, Nature vol. 344:268-270 (Mar. 1990).
Ponder, J.W., et al., “Use of Packing Criteria in the Enumeration of Allowed Sequences for Different Structural Classes”, release by Acad. Press Inc. (London) Ltd. pp. 775-791(1987).
Rappe et al., “Charge Equilibration for Molecular Dynamics Simulations,” J. Phys. Chem., 95:3358-3363 (1991).
Regan, L., “Helix is a helix is a helix?”, Proc. Natl. Acad. Sci. USA vol. 94:2796-2797 (Apr. 1997).
Smith, C.K., et al., “Guidelines for Protein Design: The Energetics of .beta. Sheet Side Chain Interactions”, Science vol. 270:980-982 (Nov. 1995).
Stickle et al., “Hydrogen Bonding in Globular Proteins,” (1992) Journal of Molecular Biology, vol. 226, pp. 1143-1159.
Sun, S., et al., “Designing amino acid sequences to fold with good hydrophobic cores”, Protein Eng. vol. 8(12):1205-1213 (1995).
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