Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

Journal of Computational Chemistry

Volumn 25, Issue 16, 2004, Pages 1937-1952

  Corcho, Francesc J ^a   Canto, Josep ^a   Perez, Juan J ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

AMBER; Molecular dynamics; Peptide folding; Simulated annealing; Substance P

Indexed keywords

CHEMICAL ANALYSIS; INFORMATION THEORY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PERMITTIVITY; SIMULATED ANNEALING; SOLUTIONS; TEMPERATURE DISTRIBUTION;

CHEMICAL RESIDUES; HYDROPHYLIC ENVIRONMENT; PEPTIDE FOLDING; WATER MOLECULES;

CONFORMATIONS;

SUBSTANCE P; WATER;

ALGORITHM; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; METHODOLOGY; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

ALGORITHMS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN FOLDING; SUBSTANCE P; THERMODYNAMICS; WATER;

EID: 9244219576     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20114     Document Type: Article

References (30)

1. Hökfelt, T.; Pernow, B.; Wahren, J. J Intern Med 2001, 249, 27.
2. Perez, J. J.; Corcho, F.; Llorens, O. Curr Med Chem 2002, 9, 2209.
3. Chassaing, G.; Convert, O.; Lavielle, S. Eur J Biochem 1986, 154, 77.
4. Sumner, S. C.; Gallagher, K. S.; Davis, D. G.; Covell, D. G.; Jernigan, R. L.; Ferretti, J. A. J Biomol Struct Dyn 1990, 8, 687.
5. Patel, A. B.; Srivastava, S.; Phadke, R. S. J Biomol Struct Dyn 2001, 19, 129.
6. Mehlis, B.; Boehm, S.; Bechker, M.; Bienert, M. Biochem Biophys Res Commun 1975, 66, 1447.
7. Mehlis, B.; Rueger, M.; Becker, M.; Bienert, N.; Niedrich, H.; Oehme, P. Int J Pept Protein Res 1980, 15, 20.
8. Miyazawa, T. Kagaku Kyoiku 1984, 32, 18.
9. Schwyzer, P.; Erne D.; Rolka, K. Helv Chim Acta 1986, 69, 1789.
10. Erne, D.; Rolka, K.; Schwyzer, R. Helv Chim Acta 1986, 69, 1807.
11. Rolka, K.; Erne, D.; Schwyzer R. Helv Chim Acta 1986, 69, 1798.
12. Wiliams, R. W.; Weawer, J. L. J Biol Chem 1990, 265, 2505.
13. Young, J. K.; Anklin, C.; Hicks, R. P. Biopolymers 1994, 34, 1449.
14. Keire, D. A.; Fletcher, T. G. Biophys J 1996, 70, 1716.
15. Nikiforovich, G. V.; Balodis, Y. Y.; Chipens, G. I. Bioorg Khim 1981, 7, 645.
16. Manavalan, P.; Momany, F. A. Pept Synth Struct Proc Am Pept Symp 7th 1981, 713.
17. Manavalan, P.; Momany, F. A. Int J Pept Protein Res 1982, 20, 351.
18. Wymore, T.; Wong, T. C. Biophys J 1999, 76, 1199.
19. Wymore, T.; Wong, T. C. Biophys J 1999, 76, 1213.
20. Coutinho, E.; Kamath, S.; Saran, A.; Srivastava, S. J Biomol Struct Dyn 1998, 16, 747.
21. Lee, S.; Suh, Y. H.; Kim, S.; Kim, Y. J Biomol Struct Dyn 1999, 17, 381.
22. Filizola, M.; Centeno, N. B.; Perez, J. J. J Pept Sci 1997, 3, 85.
23. Daura, X.; Jaun, B.; Seebach, D.; van Gusteren, W. F.; Mark, A. E. J Mol Biol 1998, 280, 925.
24. Duan, Y.; Wang, L.; Kollman, P. A. Proc Natl Acad Sci USA 1998, 95, 9897.
25. van der Spoel, D.; Berendsen, H. J. C. Biophys J 1997, 72, 2032.
26. Case, D. A.; Pearlman, D. A.; Cadwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 5, University of California, San Francisco, 1997.
27. Weiner, S. J.; Kollman, P. A.; Nguyen D. T.; Case, D. A. J Comput Chem 1986, 7, 230.
28. Srinivasan, R.; Rose, G. D. Proc Natl Acad Sci USA 1999, 96, 14258.
29. Law, G. Clustering of Archaelogical Entities-An information Theory based Approach 1999. Retrieved February 2000 from: http://www. lawas.co.nz/PAPERS/ CLUSTPAP/CLUSTPAP.HTM.
30. Corcho, F. J.; Flilizola, M.; Perez, J. J. J Biomol Struct Dyn 2000, 17, 739.