A parallel genetic algorithm for polypeptide three dimensional structure prediction. A transputer implementation

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 2, 1996, Pages 258-269

  Del Carpio, Carlos Adriel ^a  

^a TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000223085     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci950106r     Document Type: Article

References (20)

1. Anfinsen, C. The Molecular Basis of Evolution; John Wiley & Sons: 1959.
2. Holley, L. H.; Karplus, M. [10] Neural Networks for Protein Structure Prediction. Methods Enzymol. 1991, 202, 204-224.
3. Davis, L. Handbook of Genetic Algorithm: Van Unestranged Reynold: 1991.
4. Le Grand, S. M.; Merz, K. M., Jr. The application of the Genetic Algorithm to the minimization of potential energy functions. J. Global Optimization 1993, 3, 49-66.
5. Dandekar, T.; Argos, P. Potential of Genetic Algorithms in Protein Folding and Protein engineering simulations. Protein Engineering 1992, 5, 637-645.
6. Weissman, J. S.; Kim, P. S. Reexamination of the Folding of BPTI: Predominance of Native Intermediates. Science 1991, 253, 1386-1393.
7. Del Carpio, C. A., manuscript in preparation.
8. Goldberg, D. E. Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley Publishing Company, Inc.: 1989.
9. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekhara, V. Stereo-chemistry of Polypeptide Chain Configurations. J. Mol. Biol. 1963, 7, 95-99.
10. Hopfinger, A. J. Conformational Properties of Macromolecules; Academic Press: 1973.
11. Burkert, U.; Allinger, N. L. Molecular Mechanics; American Chemical Society: 1982.
12. Allinger, N. L. Calculation of Molecular Structure and Energy by Force-Field Methods. Adv. Phys. Org. Chem. 1976. 13, 1-82.
13. Allinger, N. L. Operating Instructions for the MM3 Program; 1992, 105.
14. Cramer, C. J.; Truhlar, D. G. General Parameterized SCF Model for Free Energies of Solvation in Aqueous Solution. J. Am. Chem. Soc. 1991, 113, 8305.
15. Richmond, T. J. Solvent Accessible Surface Area and Excluded Volume in Proteins. J. Mol. Biol. 1984, 178, 63-89.
16. Lee, C.; Subbiah, S. Prediction of Protein Side-chain Conformation by Packing Optimization. J. Mol. Biol. 1991, 217, 373.
17. Pickett, S. D.; Sternberg, M. J. E. Empirical Scale of Side-chain Confonnational Entropy in Protein Folding. J. Mol. Biol. 1993, 231, 825-839.
18. Allinger, N. L.; Tribble, M. T.; Miller, M. A.; Wertz, D. H. Conformational Analysis. LXIX. An Improved Force Field for the Calculation of the Structures and Energies of Hydrocarbons. J. Am. Chem. Soc. 1971, 93, 1637-1648.
19. Quadputer Owner's Manual: Microway, Inc.; 1993.
20. ic are the Cartesian coordinates for corresponding atoms of the crystal structure.