Bibliography

1

Anfinsen, C., Haber, E., Sela, M. & White, F. (1961).
The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain.
Proc. Natl. Acad. Sci. U.S.A. 47, 1309-1314.

2

Anfinsen, C. (1973).
Principles that govern the folding of protein chains.
Science 181.

3

Lim, V. (1974).
Algorithms for prediction of $\alpha$-helices and $\beta$-structural regions in globular proteins.
J.Mol.Biol. 88, 873-894.

4

Garnier, J., Osguthorpe, D. & Robson, B. (1978).
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins.
J.Mol.Biol. 120, 97-120.

5

Chou, P. & Fasman, G. (1978).
Empirical predictions of protein conformation.
Ann. Rev. Biochem. 47, 251-276.

6

Qian, N. & Sejnowski, T. (1988).
Predicting the secondary structure of globular proteins using neural network models.
J. Mol. Biol. 202, 865-884.

7

Cohen, F., Sternberg, M. & Taylor, W. (1980).
Analysis and prediction of protein $\beta$-sheet structures by a combinatorial approach.
Nature 285, 378-382.

8

Finkelstein, A. V. (1997).
Protein structure: what is possible to predict now?
Curr. Opin. Struct. Biol. 7, 61-71.

9

Shakhnovich, E. I. (1997).
Theoretical studies of protein folding thermodynamics and kinetics.
Curr. Opin. Struct. Biol. 7, 29-40.

10

Jennings, P. A. & Wright, P. E. (1993).
Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin.
Science 262, 892-896.

11

Fersht, A. R. (1995).
Characterizing transition states in protein folding: an essential step in the puzzle.
Curr. Opin. Struct. Biol. 5, 79-84.

12

Eaton, W. A., Muñoz, V., Thompson, P. A., Chan, C.-K. & Hofrichter, J. (1997).
Submillisecond kinetics of protein folding.
Curr. Opin. Struct. Biol. 7, 10-14.

13

Dill, K. et al. (1995).
Principles of protein folding - a perspective from simple exact models.
Protein Sci. 4, 561-602.

14

Bryngelson, J., Onuchic, J., Socci, N. & Wolynes, P. (1995).
Funnels, pathways, and the energy landscape of protein folding: A synthesis.
Proteins: Struct. Funct. Genet. 21, 167-195.

15

Chan, H. & Dill, K. (1993).
Energy landscape and the collapse dynamics of homopolymers.
J. Chem. Phys. 3, 2116-2127.

16

Chan, H. & Dill, K. (1994).
Transition states and folding dynamics of proteins and heteropolymers.
J. Chem. Phys. 100, 9238-9256.

17

Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1994).
Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations.
J. Chem. Phys. 101, 6052-6062.

18

Levinthal, C. (1969).
How to fold graciously.
In Mossbauer spectroscopy in biological systems ( DeBrunner, P., Tsibris, J. & Munck, E., eds.), pp. 22-24. University of Illinois Press.

19

Leopold, P., Montal, M. & Onuchic, J. (1992).
Protein folding funnels: A kinetic approach to the sequence-structure relationship.
Proc. Natl. Acad. Sci. USA 89, 8721-8725.

20

Dill, K. & Chan, H. (1997).
From levinthal to pathways to funnels.
Nat. Struct. Biol. 4, 10-19.

21

Goldstein, R., Luthey-Schulten, Z. & Wolynes, P. (1992).
Optimal protein-folding codes from spin-glass theory.
Proc. Natl. Acad. Sci. USA 89, 4918-4922.

22

Sali, A., Shakhnovich, E. & Karplus, M. (1994).
Kinetics of protein folding - A lattice model study of the requirements for folding to the native state.
J. Mol. Biol. 235, 1614-1636.

23

Shakhnovich, E. & Gutin, A. (1993).
Engineering of stable and fast-folding sequences of model proteins.
Proc. Natl. Acad. Sci. USA 90, 7195-7199.

24

Shakhnovich, E. & Gutin, A. (1993).
A new approach to the design of stable proteins.
Protein Eng. 6, 793-800.

25

Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1994).
Specific nucleus as the transition state for protein folding: Evidence from the lattice model.
Biochemistry 33, 10026-10036.

26

Shakhnovich, E. I. (1994).
Proteins with selected sequences fold into unique native conformation.
Phys. Rev. Lett. 72, 3907-3910.

27

Kolinski, A., Godzik, A. & Skolnick, J. (1993).
A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins.
J. Chem. Phys. 98, 7420-7433.

28

Miyazawa, S. & Jerningan, R. (1985).
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation.
Macromolecules 18, 534-552.

29

Sippl, M. J. (1990).
Calculation of conformational ensembles from potentials of mean force.
J. Mol. Biol. 213, 859-883.

30

Pereira de Araújo, A. F. & Pochapsky, T. C. (1996).
Monte Carlo simulations of protein folding using inexact potentials: How accurate must parameters be in order to preserve the essential features of the energy landscape?
Folding & Design 1, 299-314.

31

Pereira de Araújo, A. F. & Pochapsky, T. C. (1997).
Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments.
Folding & Design 2, 135-139.

32

Binder, K. & Heermann, D. (1988).
Monte Carlo simulation in statistica physics.
Springer-Verlag.

33

Metropolis, N., Rosembluth, A., Rosembluth, M. & Teller, A. (1953).
Equation os state calculations by fast computing machines.
J. Chem. Phys. 21, 1087-1092.

34

Socci, N. & Onuchic, J. (1995).
Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique.
J. Chem. Phys. 103, 4732-4744.

35

Sali, A., Shakhnovich, E. & Karplus, M. (1994).
How does a protein fold?
Nature 369, 248-251.

36

Levitt, M. (1976).
A simplified representation of protein conformations for rapid simulation of protein folding.
J. Mol. Biol. 104, 59-107.

37

Covell, D. G. (1992).
Folding protein $\alpha$-carbon chains into compact forms by monte carlo methods.
Proteins: Struct. Funct. Genet. 14, 409-420.

38

Skolnick, J. & Kolinski, A. (1990).
Simulations of the folding of a globular protein.
Science 250, 1121-1125.

39

Kolinski, A. & Skolnick, J. (1994).
Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
Proteins: Struct. Funct. Genet. 18, 353-366.

40

Godzik, A., Kolinski, A. & Skolnick, J. (1993).
Lattice representations os globular proteins: How good are they?
J. Comp. Chem. 14, 1194-1202.

41

Wilson, C. & Doniach, S. (1989).
A computer model to dynamically simulate protein folding: studies with crambin.
Proteins: Struct. Funct. Genet. 6, 193-209.

42

Karplus, M. & Shakhnovich, E. I. (1992).
Protein folding: Theoretical studies of thermodynamics and dynamics.
In Protein Folding ( Creighton, T. E., ed.), pp. 127-195. W.H. Freeman and Company, New York.

43

Privalov, P. L. (1992).
Protein Folding, chap. Physical Basis of the Stability of the Folded Conformations of Proteins.
W. H. Freeman and Company.

44

Pochapsky, T. C. & Gopen, Q. (1992).
A chromatographic approach to the determination of relative free energies of interaction between hydrophobic and amphiphilic amino acid side chains.
Protein Sci. 1, 786-795.

45

Onuchic, J., Wolynes, P., Luthey-Schulten, Z. & Socci, N. (1995).
Toward an outline of the topography of a realistic protein folding funnel.
Proc. Natl. Acad. Sci. USA 92, 3626-3630.

46

Mirny, L. A., , Abkevich, V. I. & Shakhnovich, E. I. (1996).
Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model.
Folding & Design 1, 103-116.

47

Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1995).
Domains in folding of model proteins.
Protein Sci. 4, 1167-1177.

48

Gutin, A., Abkevich, V. & Shakhnovich, E. (1995).
Is burst hydrophobic collapse necessary for protein folding ?
Biochemistry 34, 3066-3076.

49

Morrisey, M. P. & Shakhnovich, E. I. (1996).
Design of proteins with selected thermal properties.
Folding & Design 1, 391-405.

50

Fersht, A. R. (1997).
Nucleation mechanisms in protein folding.
Curr. Opin. Struct. Biol. 7, 3-9.

51

Shakhnovich, E. I., Abkevich, V. I. & Ptitsyn, O. (1996).
Conserved residues and the mechanism of protein folding.
Nature 379, 96-98.

52

Socci, N. & Onuchic, J. (1994).
Folding kinetics of proteinlike heteropolymers.
J. Chem. Phys. 101, 1519-1528.

53

de Gennes, P. G. (1990).
Introduction to polymer dynamics.
Cambridge University Press.

54

Gutin, A., Abkevich, V. & Shakhnovich, E. (1995).
Evolution-like selection of fast-folding model proteins.
Proc. Natl. Acad. Sci. USA 92, 3066-3076.

55

Betancourt, M. & Onuchic, J. (1995).
Kinetics of proteinlike models: The energy landscape factors that determine folding.
J. Chem. Phys. 103, 773-787.

56

Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1995).
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.
J. Mol. Biol. 252, 460-471.

57

Socci, N., Onuchic, J. & Wolynes, P. (1996).
Diffusive dynamics of the reaction coordinate for protein folding funnels.
J. Chem. Phys. 104, 5860-5868.

58

Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1996).
Improved design of stable and fast-folding model proteins.
Folding & Design 1, 221-230.

59

Abagyan, R. A. (1993).
Towards protein folding by global energy optimization.
FEBS Lett. 325, 17-22.

60

Bryngelson, J. (1994).
When is a potential accurate enough for structure prediction? Theory and application to a random heteropolymer model of protein folding.
J. Chem. Phys. 100, 6038-6045.

61

Finkelstein, A. V., Gutin, A. M. & Badretdinov, A. Y. (1995).
Perfect temperature for protein structure prediction and folding.
Proteins:Struct., Func. & Genet. 23, 151-162.

62

Pande, V. S., Grosberg, A. & Tanaka, T. (1995).
How accurate must potentials be for successful modeling of protein folding?
J. Chem. Phys. 103, 9482-9491.

63

Govindarajan, S. & Goldstein, R. (1994).
Searching for foldable protein structures using optimized energy functions.
Biopolymers 36, 43-51.

64

Shakhnovich, E. & Gutin, A. (1989).
Formation of unique structure in polypeptide chain. Theoretical investigation with the aid of a replica approach.
Biophys. Chem. 34, 187-199.

65

Bryngelson, J. & Wolynes, P. (1987).
Spin glasses and the statistical mechanics of protein folding.
Proc. Natl. Acad. Sci. USA 84, 7524-7528.

66

Derrida, B. (1981).
Random-energy model: An exactly solvable model of disordered systems.
Phys. Rev. B 24, 2613-2626.

67

Frauenfelder, H. & Wolynes, P. (1994).
Biomolecules: Where the physics of complexity and simplicity meet.
Physics Today 47, 58-64.

68

Pande, V. S., Grosberg, A. & Tanaka, T. (1997).
On the theory of folding kinetics for short proteins.
Folding & Design 2, 109-114.

69

Luthey-Shulten, Z., Ramirez, B. & Wolynes, P. (1995).
Helix-coil, liquid crystal, and spin glasses transitions of a collapsed heteropolymer.
J. Chem. Phys. 99, 2177-2185.

70

Baum, J., Dobson, C. M., Evans, P. A. & Hanley, C. (1989).
Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guine pig $\alpha$-lactalbumin.
Biochemistry 28, 7-13.

71

Feng, Y., Sligar, S. & Wand, A. (1994).
Solution structure of apocytochrome b₅₆₂.
Nat. Struct. Biol. 1, 30-36.

72

McCammon, J. & Harvey, S. (1987).
Dynamics of proteins and nucleic acids.
Cambridge Univ. Press, New York.

73

Hendlich, M., Gottsbacher, K., Casari, G. & Sippl, M. (1990).
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.
J Mol. Biol. 216, 167-180.

74

Jones, D., Taylor, W. & Thornton, J. (1992).
A new approach to protein fold recognition.
Nature 358, 86-89.

75

Maiorov, V. & Crippen, G. (1992).
Contact potential that recognizes the correct folding of globular proteins.
J. Mol. Biol. 227, 876-888.

76

Bryant, S. & Lawrence, C. (1993).
An empirical energy function for threading protein sequence through the folding motif.
Proteins: Struct., Funct., Genet. 16, 92-112.

77

Sun, S., Thomas, P. & Dill, K. (1995).
A simple protein folding algorithm using a binary code and secondary structure constraints.
Protein Eng. 8, 769-778.

78

Huang, E., Subbiah, S. & Levitt, M. (1995).
Recognizing native folds by the arrangement of hydrophobic and polar residues.
J. Mol. Biol. 252, 709-720.

79

Thomas, P. & Dill, K. (1996).
Statistical potentials extracted from protein structures: How accurate are they?
J. Mol. Biol. 257, 457-469.

80

Mirny, L. A. & Shakhnovich, E. I. (1996).
How to derive a protein folding potential? A new approach to the old problem.
J. Mol. Biol. 264, 1164-1179.

81

Shakhnovich, E. & Gutin, A. (1989).
Relaxation to equilibrium in the Random Energy Model.
Europhys. Lett. 9, 569-574.

82

Shakhnovich, E. & Gutin, A. (1990).
Implications of thermodynamics of protein folding for evolution of primary sequences.
Nature 93, 2043-2047.

83

Plotkin, S., Wang, J. & Wolynes, P. (1995).
Correlated energy landscape model for finite, random heteropolymers.
Phys. Rev. E 53, 6271-6296.