A fast conformational search strategy for finding low energy structures of model proteins

Protein Science

Volumn 5, Issue 10, 1996, Pages 2037-2043

  Beutler, Thomas C ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

chain growth algorithm; conformational searching; lattice model; protein folding

Indexed keywords

ALGORITHM; ARTICLE; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 0029909775     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560051010     Document Type: Article

References (38)

1. Binder K, Heermann DW. 1988. Monte Carlo simulations in statistical physics. Berlin/New York: Springer.
2. Boczko EM, Brooks CL. 1995. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 269:393-396.
3. Chan HS, Dill KA. 1991. "Sequence space soup" of proteins and copolymers. J Chem Phys 95:3775-3787.
4. Covell DG. 1992. Folding protein α-carbon chains into compact forms by Monte Carlo methods. Proteins Struct Fund Genet 14:409-420.
5. Covell DG. 1994. Lattice model simulations of polypeptide chain folding. J Mol Biol 235:1032-1043.
6. Dill KA. 1993. Folding proteins: Finding a needle in a haystack. Curr Opin Struct Biol 3:99-103.
7. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. 1995. Principles of protein folding - A perspective from simple exact models. Protein Sci 4:561-602.
8. Dill KA, Fiebig KM, Chan HS. 1993. Cooperativity in protein folding kinetics. Proc Natl Acad Sci USA 90:748-752.
9. Fiebig KM, Dill KA. 1993. Protein core assembly process. J Chem Phys 98:3475-3487.
10. Garel T, Orland H. 1990. Guided replication of random chains: A new Monte Carlo method. J Phys A 23:L621-L626.
11. Hart WE, Istrail S. 1996. Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. J Comput Biol. Forthcoming.
12. Hinds D, Levitt M. 1994. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 243:668-682.
13. Kolinski A, Skolnick J. 1994. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins Struct Funct Genet 18:338-352.
14. Kuntz ID, Crippen GM, Kollman PA, Kimelman D. 1976. Calculation of protein tertiary structure. J Mol Biol 106:983-994.
15. Lau KF, Dill KA. 1989. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 22:3986-3997.
16. Levitt M, Warshel A. 1975. Computer simulation of protein folding. Nature 253:694-698.
17. Meirovitch U. 1977. Calculation of entropy with computer simulation methods. Chem Phys Lett 45:389-392.
18. Meirovitch H. 1983a. Improved computer simulation method for estimating the entropy of macromolecules with hard-core potential. Macromolecules 16:1628-1631.
19. Meirovitch H. 1983b. Method for estimating the entropy of macromolecules with computer simulation. Chains with excluded volume. Macromolecules 16:249-252.
20. Meirovitch H. 1985. Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks. Phys Rev A 32:3699-3708.
21. Meirovitch H, Livne S. 1988. Computer simulation of long polymers adsorbed on a surface. I. Corrections to scaling in an ideal chain. J Chem Phys 88:4498-4506.
22. Monge A, Friesner RA, Honig B. 1994. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc Natl Acad Sci USA 91:5021-5029.
23. O'Toole EM, Panagiotopoulos AZ. 1992. Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm. J Chem Phys 97:8644-8652.
24. Rosenblmh MN, Rosenbluth AW. 1955. Monte Carlo calculation of the average extension of molecular chains. J Chem Phys 23:356-359.
25. Sippl M, Hendlich M, Lackner P. 1992. Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4. Protein Sci 1:625-640.
26. Skolnick J, Kolinski A. 1990. Simulations of the folding of a globular protein. Science 250:1121-1125.
27. Solomon JE, Liney D. 1995. Exploration of compact protein conformations using the guided replication Monte Carlo method. Biopolymers 36:579-591.
28. Sosnick TR, Mayne L, Hiller R, Englander SW. 1994. The barriers in protein folding. Nature Struct Biol 1:149-156.
29. Srinivasan R, Rose GD. 1995. LINUS - A hierachic procedure to predict the fold of a protein. Proteins Struct Funct Genet 22:81-99.
30. Sun S, Thomas PD, Dill KA. 1995. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 8:769-778.
31. Toma L, Toma S. 1996. Contact interactions method: A new algorithm for protein folding simulations. Protein Sci 5:147-153.
32. Unger R. Moult J. 1993. Genetic algorithms for protein folding simulations. J Mol Biol 231:75-81.
33. Vajda S, Jafri MS, Sezerman OU, DeLisi C. 1993. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers 33:173-192.
34. Wallqvist A, Ullner M, Covell DG. 1994. A simplified amino acid potential for use in structure predictions of proteins. Proteins Struct Funct Genet 18:267-280.
35. Wilson C, Doniach S. 1989. A computer model to dynamically simulate protein folding - Studies with crambin. Proteins Struct Funct Genet 6:193-209.
36. Yue K, Dill KA. 1993. Sequence-structure relationships in proteins and copolymers. Phys Rev E 48(3):2261-2278.
37. Yue K, Dill KA. 1996. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci 5:254-261.
38. Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. 1995. A test of lattice protein folding algorithms. Proc Natl Acad Sci USA 92:325-329.