Generalized simulated annealing applied to protein folding studies

Journal of Computational Chemistry

Volumn 27, Issue 11, 2006, Pages 1142-1155

  Agostini, Flavia P ^a   Soares Pinto, Diogo De O ^b   Moret, Marcelo A ^c,d   Osthoff, Carla ^a   Pascutti, Pedro G ^e  

^a LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^b CENTRO BRASILEIRO DE PESQUISAS FÍSICAS   (Brazil)

^c Fundacao Visconde de Cairu   (Brazil)

^d DEPARTAMENTO DE CIÊNCIAS BIOLÓGICAS   (Brazil)

^e FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

Generalized simulated annealing; Global optimization; Grid based platform; Protein folding; Tsallis' statistics

Indexed keywords

AMINO ACIDS; CHEMICAL BONDS; DEGREES OF FREEDOM (MECHANICS); GLOBAL OPTIMIZATION; MOLECULAR BIOLOGY; SIMULATED ANNEALING;

GENERALIZED SIMULATED ANNEALING; GRID-BASED PLATFORM; PROTEIN FOLDING; TSALLIS' STATISTICS;

PROTEINS;

PEPTIDE; POLYALANINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE;

AMINO ACID MOTIFS; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY;

EID: 33745880405     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20428     Document Type: Article

References (31)

1. Yon, J. M. Cell Mol Life Sci 1997, 53, 557.
2. Tsallis, C.; Stariolo, D. A. Physica A 1996, 233, 395.
3. Stariolo, D. A.; Tsallis, C. In Annual Reviews of Computational Physics; Stauffer, D., Ed.; World Scientific: Singapore, 1995, p. 343, vol. II.
4. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
5. Szu, H.; Hartley, R. Phys Lett A 1987, 122, 157.
6. Moret, M. A.; Bisch, P. M.; Vieira, F. M. C. Phys Rev E 1998, 57, R2535.
7. Moret, M. A.; Pascutti, P. G.; Bisch, P. M.; Mundim, K. C. J Comp Chem 1998, 19, 647.
8. Mundim, K. C.; Tsallis, C. Int J Quantum Chem 1996, 58, 373.
9. Mundim, K. C.; Lemaire, T.; Bassrei, A. Physica A 1998, 252, 405.
10. Dorfman, S.; Liubich, V.; Fuks, D.; Mundim, K. C. J Phys Condens Matter 2001, 13, 6719.
11. Fuks, D.; Dorfman, S.; Mundim, K. C.; Ellis, D. E. Int J Quantum Chem 2001, 85, 354.
12. Fuks, D.; Mundim, K. C.; Malbouisson, L. A. C.; Berner, A.; Dorfman, S.; Ellis, D. E. J Mol Struct 2001, 539, 199.
13. Berner, A.; Mundim, K. C.; Ellis, D. E.; Dorfman, S.; Fuks, D.; Evenhaim, R. Sensors Actuators 1999, 74, 86.
14. Penna, T. J. P. Phys Rev E 1995, 51, R1.
15. Penna, T. J. P. Comp Phys 1995, 9, 341.
16. Cirne, W.; Marzullo, K. Proceedings of the 13th Symposium on Computer Architecture and High Performance Computing, 2001.
17. Agostini, F. P.; Osthoff, C.; Vassalo, A.; Pinto, D. S.; Pascutti, P. G. Rev Technol Inform Bras 2003, 3, 103.
18. Moret, M. A.; Bisch, P. M.; Mundim, K. C.; Pascutti, P. G. Biophys J 2002, 82, 1123.
19. Dall'Igna, A., Jr.; Silva, R. S.; Mundin, K. C.; Dardenne, L. E. Genet Mol Biol 2004, 27, 616.
20. Zhou, Y.; Karplus, M. J Mol Biol 1994, 293, 917.
21. Zhou, Y.; Karplus, M. Nature 1999, 401, 400.
22. Dandekar, T.; Argos, P. J Mol Biol 1994, 236, 844.
23. Uk, B.; Taufer, M.; Stricker, T.; Settanni, G.; Cavalli, A.; Caflisch, A. Darthmouth University Technical Report TR2003-38, 2003.
24. Uk, B.; Taufer, M.; Stricker, T.; Settanni, G.; Cavalli, A. Darthmouth University Technical Report TR2003-385, 2003.
25. Cirne, W.; Paranhos, D.; Costa, L.; Santos-Neto, E.; Brasileiro, F.; Sauvé, J.; Silva, F.; Osthoff, C. 5th International Conference in Parallel Processing, Taiwan, 2003.
26. Andricioaei, I.; Straub, J. E. Phys Rev E 1996, 53, R3055.
27. Hansmann, U. H. E. Physica A 1997, 242, 250.
28. Hansmann, U. H. E. Comp Phys Commun 2002, 147, 604.
29. Hansmann, U. H. E. Phys Rev E 2004, 70, 01290.
30. Hansmann, U. H. E.; Okamoto, Y. Bras J Phys 1999, 29, 187.
31. Whitfield, L. B.; Straub, J. E. Physica A 2002, 305, 157.