Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2007-06-12
2007-06-12
Moran, Marjorie A. (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C703S011000, C702S027000
Reexamination Certificate
active
09877695
ABSTRACT:
Methodology for the automated design of proteins is disclosed. Various methods executed by a computer for generating probability matrices, protein sequences, combinatorial libraries of proteins, and optimization of various parameters related to protein design are disclosed. Methodology is applicable to the design and analysis of protein structures and protein sequences.
REFERENCES:
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: 2002/0123846 (2002-09-01), Miller et al.
Shaojian Sun. “Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms.”Protein Science. (1993), 2, 762-785.
Fujiyoshi-Yoneda. “Adaptability of restrained molecular dynamics for tertiary structure prediction: application to Crotalus atrox venom phospholipase A2.”Protein Engineering. (1991), vol. 4, 443-450.
International Search Report. PCT/US02/03789, mailed Jan. 22, 2003.
Dahiyat et al. “Automated design of the surface positions of protein helices.”Protein Science. (1997), 6: 1333-1337.
Dahiyat et al. “Protein design automation.”Protein Science. (1996), 5: 895-903.
Dahiyat et al. “De novo protein design: Fully automated sequence selection.”Science. vol. 278, Oct. 3, 1997, 82-87.
Dahiyat et al. “Probing the role of packing specificity in protein design.”Proc. Natl. Acad. Sci. USA. vol. 94, 10172-10177, Sep. 1997.
Dahiyat et al. “De novo protein design: Towards fully automated sequence selection.”J. Mol. Biol. (1997) 273, 789-796.
Delarue et al. “The inverse protein folding problem: Self consistent mean field optimisation of a structure specific mutation matrix.”Pac Symp Biocomput. (1997), 109-121.
Desjarlais et al. “Computer Search Algorithms in protein modification and design.” (1998)Curr Opin Struct Biol. 8(4). 471-5.
Desjarlais et al. “De novo design of the hydrophobic cores of proteins.”Protein Science(1995), 4, 2006-18.
Desjarlais et al. Side-chain and backbone flexibility in protein core design.J. Mol. Biol. (1999), 290(1), 305-18.
Desmet et al., “The dead-end elimination theorem and its use in protein side-chain positioning.”Nature. (1992), 356(9), 539-542.
Dunbrack et al. Bayesian statistical analysis of protein side-chain rotamer preferences.Protein Sci. (1997), 6(8), 1661-81.
Eisenberg et al., “Solvation energy in protein folding and binding,”Nature. 319, 199-203, 1986.
Goldstein. Efficient rotamer elimination applied to protein side-chains and related spin glasses.Biophys. J. (1994), 66(5), 1335-40.
Gordon. Energy functions for protein design.Curr Opin Struct Biol. (1999), 9(4), 509-13.
Harbury et al. “Repacking protein cores with backbone freedom: structure prediction for coiled coils.”Proc Natl Acad Sci USA. (1995), 92(18), 8408-12.
Hellinga. “Rational protein design: combining theory and experiment.”Proc Natl Acad Sci USA. (1997), 94(19), 10015-17.
Hellinga et al. “Optimal sequence selection in proteins of known structure by simulated evolution.”Proc Natl Acad Sci USA. (1994), 91(13), 5803-7.
Hendsch et al. Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding.Protein. Sci. (1999), 8(7), 1381-92.
Henikoff et al. Position-based sequence weights.J. Mol. Biol. (1994), 243(4), 574-8.
Holland.Adaptation in natural and artificial systems. The MIT Press, Cambridge, MA (1992).
Johnson et al. Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.Structure Fold Des. (1999), 7(8), 967-76.
Jorgensen et al. “The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin.”J. Amer. Chem. Soc. (1988), 110(6), 1657-1666.
Koehl et al. “Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.”J. Mol. Biol., 239(2), 249-75.
Koehl et al. “Mean-field minimization methods for biological macromolecules.”Curr Opin Struct Biol., (1996), 6(2), 222-6.
Kono et al. “Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.”Proteins. (1994), 19(3), 244-255.
Kono et al. “Designing the hydrophobic core of Thermus flavus malate dehydrogenase based on side-chain packing.”Protein Eng. (1998), 11(1), 47-52.
Kuhlman et al. “Native protein sequences are close to optimal for their structures.”Proc. Natl. Acad. Sci. USA. (2000), 97(19), 10383-8.
Lazar et al. “De novo design of the hydrophobic core of ubiquitin.”Protein Sci. (1997), 6(6), 1167-78.
Lazar et al. “Rotamer strain as a determinant of protein structural specificity.”Protein Sci. (1999), 8(12), 2598-610.
Lee. “Predicting protein mutant energetics by self-consistent ensemble optimization.”J. Mol. Biol. (1994), 236(3), 918-39.
Micheletti et al. “Design of proteins with hydrophobic and polar amino acids.”Proteins. (1998), 32(1), 80-7.
Raha et al. “Prediction of amino acid sequence from structure.”Protein Sci. (2000), 9(6), 1106-19.
Ranganathan et al. “Structural and functional analysis of the mitotic rotamase Pin 1 suggests substrate recognition is phosphorylation dependent.”Cell. (1997), 89(6), 875-86.
Street et al. “Computational protein design.”Structure Fold Des. (1999), 7(5), R105-9.
Su et al. “Coupling backbone flexibility and amino acid sequence selection in protein design.”Protein Sci. (1997), 6(8), 1701-7.
Voigt et al. “Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design.”J. Mol. Biol. (2000), 299(3), 789-803.
Voight et al. “Computational method to reduce the search space for directed protein evolution.”Proc. Natl. Acad. Sci. USA. (2001), 98(7), 3778-83.
Weiner et al. “A new force field for molecular mechanical simulation of nucleic acids and proteins.”Journal of the American Chemicical Society. (1984), 106(3), 765-84.
Fish & Richardson P.C.
Moran Marjorie A.
The Penn State Research Foundation
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