Protein design automation for protein libraries

Details Protein design automation for protein libraries Protein design automation for protein libraries

2003-09-18

2008-05-27

Borin, Michael (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S027000, C706S045000, C706S046000

Reexamination Certificate

active

07379822

ABSTRACT:
The invention relates to the use of protein design automation (PDA) 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: 5884230 (1999-03-01), Srinivasan 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: 6708120 (2004-03-01), Mayo et al.
patent: 2001/0032052 (2001-10-01), Mayo et al.
patent: 2001/0039480 (2001-11-01), Mayo et al.
patent: 2002/0004706 (2002-01-01), Mayo et al.
patent: 2002/0048772 (2002-04-01), Dahiyat et al.
patent: 2002/0072864 (2002-06-01), Lacroix et al.
patent: 2002/0090648 (2002-07-01), Dahiyat et al.
patent: 2002/0106694 (2002-08-01), Mayo et al.
patent: 2003/0049654 (2003-03-01), Dahiyat et al.
patent: 2003/0130827 (2003-07-01), Bentzien et al.
patent: 2004/0043429 (2004-03-01), Dahiyat et al.
patent: 0549107 (1993-06-01), None
patent: 0 974 111 (2000-01-01), None
patent: WO 95/22625 (1995-08-01), None
patent: WO 98/05765 (1998-02-01), None
patent: WO 98/32845 (1998-07-01), None
patent: WO 98/32845 (1998-07-01), None
patent: WO 98/47089 (1998-10-01), None
patent: WO 00/23564 (2000-04-01), None
patent: WO 00/40715 (2000-07-01), None
patent: WO 00/68396 (2000-11-01), None
patent: WO 00/68396 (2000-11-01), None
patent: WO 01/37147 (2001-05-01), None
patent: WO 01/39098 (2001-05-01), None
patent: WO 01/59066 (2001-08-01), None
patent: WO 01/59066 (2001-08-01), None
patent: WO 01/61344 (2001-08-01), None
patent: WO 03/006154 (2003-01-01), None
patent: WO 03/014325 (2003-02-01), None
patent: WO 03/014325 (2003-02-01), None
patent: WO 94/16090 (2004-07-01), None
Altshul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Research, 1997, 25, 3389-3402.
Srinivasan et al. Biomacromolecules: From 3-D to Applications, Hanford Symposium on Health and the Environment, 34th, Pasco, Wash., Oct. 23-26, 1995 (1997), Meeting Date 1995, 69-81. Editor(s): Ornstein, Rick L. Publisher: Battelle Press, Columbus, Ohio.
Levitt et al. Biochemistry, 1978, 17, 4277-4284.
Topham et al. J. Mol. Biol., 194-220, 1993.
Borman, “Proteins to Order,” C&EN, 1997, pp. 9-10.
Bowie et al., “A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure,” Science, 1991, 253(5016):164-170.
Bowie et al., “Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions,” Science, 1990, 247:1306-1310.
Brenner et al., “A quantitative methodology for the de novo design of proteins,” Protein Science, 1994, 3:1871-1882.
Brooks et al., “CHARMM: A program for Macromolecular Energy, Minimization, and Dynamics Calculations,” Journal of Computational Chemistry, 1983, 4(2):187-217.
Connolly, “Solvent-Accessible Surfaces of Proteins and Nucleic Acids,” Science, 1983, 221(4612):709-713.
Cornell et al., “A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules,” J. Am. Chem. Soc., 1995, 117:5179-5197.
Dahiyat et al., “Protein Design Automation,” Protein Science, 1995, 4(2):83.
Dahiyat et al., “Automated design of the surface positions of protein helices,” Protein Science, 1997, 6:1333-1337.
Dahiyat et al., “De Novo Protein Design: Fully Automated Sequence Selection,” Science, 1997, 278:82-87.
Dahiyat et al., “First Fully Automatic Design of a Protein Achieved by Caltech Scientists,” Caltech Media Relations Press Release, 1997, pp. 1-2.
Dahiyat et al., “Probing the Role of Specificity in Protein Design,” Caltech Biology Annual Report, 1996, pp. 160-161.
Dahiyat et al., “Protein design automation,” Caltech Biology Annual Report, 1995, p. 172.
Dahiyat et al., “Protein design automation,” Protein Science, 1996, 5:895-903.
Dahiyat et al., “Protein Design Automation,” Prot. Science, Poster Sessions, 1996, 5(1):22-23.
Dalal et al., “Protein alchemy: Changing β-sheet into α-helix,” Nature Structural Biology, 1997, 4(7):548-552.
Degrado, “Proteins from Scratch,” Science, 1997, 278:80-81.
Desjarlais et al., “De novo design of the hydrophobic cores of proteins,” Protein Science, 1995, 4(10):2006-2018.
Desjarlais et al., “New strategies in protein design,” Current Opinion in Biotechnology, 1995, 6:460-466.
Desmet et al., “The dead-end elimination theorem and its use in protein side-chain positioning,” Nature, 1992, 356(9):539-542.
Desmet et al., “Theoretical and Algorithmic Optimization of the Dead-End Elimination Theorem,” Proceedings of the Pacific Symposium on Biocomputing '97, 1997, pp. 123-133.
Desmet et al., The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem, The Protein Folding Problem and Tertiary Structure Prediction, 1994, Ch. 10:1-49.
Dunbrack et al., “Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains,” Nat. Struct. Biol., 1994, 1(5):334-40.
Eisenberg et al., “Solvation energy in protein folding and binding,” Nature, 1986, 319:199-203.
Fechteler et al., “Prediction of Protein Three-dimensional Structures in Insertion and Deletion Regions: A Procedure for Searching Data Bases of Representative Protein Fragments Using Geometric Scoring Criteria,” J. Mol. Biol., 1995, 253:114-131.
Gallop et al., “Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries,” Journal of Medicinal Chemistry, 1994, 37(9):1233-1251.
Goldstein, “Efficient rotamer elimination applied to protein side-chains and related spin glasses,” Biophysics Journal, 1994, 66(5):1335-1340.
Gordon et al., “Energy functions for protein design,” Current Opinion in Structural Biology, 1999, 9:509-513.
Harbury et al., “High-Resolution Protein Design with Backbone Freedom,” Science, 1998, 282:1462-1467.
Harbury et al., “Repacking protein cores with backbone freedom: Structure prediction for coiled coils,” Proceedings of the National Academy of Sciences, USA, 1995, 92:8408-8412.
Hellinga et al., “Construction of New Ligand Binding Sites in Proteins of Known Structure I. Computer-aided Modeling of Sites with Pre-defined Geometry,” Journal of Molecular Biology, 1991, 222:763-785.
Hellinga et al., “Optimal sequence selection in proteins of known structure by simulated evolution,” Proceedings of the National Academy of Sciences USA, 1994, 91:5803-5807.
Hellinga, “Rational protein design: Combining theory and experiment,” Proceedings of the National Academy of Sciences, USA, 1997, 94:10015-10017.
Holmes, “First-ever designer protein fits like a glove,” New Scientist, 1997, pp. 1-2.
Hurley et al., “Design and Structural Analysis of Alternative Hydrophobic Core Packing Arrangements in Bacteriophage T4 Lysozyme,” Journal of Molecular Biology, 1992, 224:1143-1159.
Jones, “De novo protein design using pairwise potentials and a genetic algorithm,” Protein Science, 1994, 3:567-574.
Koehl et al., “De Novo Protein Design 1. In Search of Stability and Specificity,” Journal of Molecular Biology, 1999, 293:1161-1181.
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 , 1994, 19(3):244-255.
Kortemme et al., “Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein,” Science, 1998, 28

Affiliated with

Also associated with

Rating

Protein design automation for protein libraries does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Protein design automation for protein libraries, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Protein design automation for protein libraries will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3985176