Contact interactions method: A new algorithm for protein folding simulations

Protein Science

Volumn 5, Issue 1, 1996, Pages 147-153

  Toma, Lucio ^a   Toma, Salvatore ^b  

^a UNIVERSITY OF PAVIA   (Italy)

^b BioScience Center   (Italy)

Author keywords

conformational search algorithm; hydrophobic interactions; lattice models; protein folding

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER SIMULATION; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; SYSTEM ANALYSIS;

EID: 0030034935     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050118     Document Type: Article

References (25)

1. Abkevich VI, Gutin AM, Shakhnovich EI. 1994a. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33:10026-10036.
2. Abkevich VI, Gutin AM, Shakhnovich EI. 1994b. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J Chem Phys 101:6052-6062.
3. Camacho CJ, Thirumalai D. 1993. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 90:6369-6312.
4. Covell DG. 1994. Lattice model simulations of polypeptide chain folding. J Mol Biol 235:1032-1043.
5. Dandekar T, Argos P. 1994. Folding the main chain of small proteins with the genetic algorithm. J Mol Biol 236:844-861.
6. 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.
7. Dill KA, Fiebig KM, Chan HS. 1993. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 90:1942-1946.
8. Fiebig KM, Dill KA. 1993. Protein core assembly processes. J Chem Phys 98:3475-3481.
9. Gutin AM, Abkevich VI, Shakhnovich EI. 1995a. Evolution-like selection of fast-folding model proteins. Proc Natl Acad Sci USA 92:1282-1286.
10. Gutin AM, Abkevich VI, Shakhnovich EI. 1995b. Is burst hydrophobic collapse necessary for protein folding? Biochemistry 54:3066-3076.
11. Hunt NG, Gregoret LM, Cohen FE. 1994. The origin of protein secondary structure. Effects of packing density and hydrogen bonding studies by a fast conformational search. J Mol Biol 241:214-225.
12. Lattman EE, Fiebig KM, Dill KA. 1994. Modeling compact denaturated states of proteins. Biochemistry 33:6158-6166.
13. Levinthal C. 1968. Are there pathways for protein folding? J Chem Phys 65:44-45.
14. Madras N, Sokal AD. 1988. The pivot algorithm: A highly efficient Monte Carlo method for self-avoiding walk. J Stat Phys 50:109-186.
15. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. 1953. Equation of state calculations by fast computing machine. J Chem Phys 21:1087-1092.
16. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. 1995. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci USA 92:3626-3630.
17. Sali A, Shakhnovich EI, 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.
18. Shakhnovich EI, Gutin AM. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA 90:7195-7199.
19. Socci ND, Onuchic JN. 1994. Folding kinetics of proteinlike heteropolymers. J Chem Phys 101:1519-1528.
20. Stellman SD, Gans PJ. 1972. Efficient computer simulation of polymer conformation. I. Geometric properties of hard-sphere model. Macromolecules 5:516-526.
21. Sun S. 1993. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci 2:762-785.
22. Unger R, Moult J. 1993. Genetic algorithms for protein folding simulations. J Mol Biol 237:75-81.
23. Yee DP, Chan HS, Havel TF, Dill KA. 1994. Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. J Mol Biol 241:551-513.
24. Yue K, Dill KA. 1995. Forces of tertiary structural organization of globular proteins. Proc Natl Acad Sci USA 92:146-150.
25. 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.