A constraint-based approach for deriving 3-D structures of cyclic polypeptides

Constraints

Volumn 6, Issue 2-3, 2001, Pages 257-269

  Rodošek, Robert ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Constraint reasoning; Optimisation problems; Protein folding problems; Simulated annealing

Indexed keywords

EID: 0342902148     PISSN: 13837133     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1011437706814     Document Type: Article

References (12)

1. Aarts, E. H., Van Laarhoven, P. J. M., Lenstra, J. K., & Ulder, N. L. J. (1994). A computational study of local search algorithms for job shop scheduling. Journal of Computing, 6(2): 118-125.
2. APPLAUSE: application & assessment of parallel programming using logic. (1993). In Proceedings of PARLE'93, Conference on Parallel Architectures and Languages Europe.
3. Benhamou, F., & Older, W. (1995). Applying interval arithmetic to real, integer and boolean constraints. Journal of Logic Programming.
4. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M., (1983). CHARMM: a program for macromolecular energy, minimization, and dynamic calculations. Journal of Computational Chemistry, 4(2): 187-217.
5. Brandn, C., & Tooze, J. (1991). Introduction to Protein Structure. Garland Publishing, Inc.
6. ECLiPSe User Manual, Version 3.7.1. (1998). London: IC-Parc, Imperial College.
7. Kirkpatrick, S., Gelatt, C. D., & Vecchi, M. P. (1983). Optimization by simulated annealing. Science, 220: 671-680.
8. Kostrowicki, J., & Scheraga, H. A. (1996). Some approaches to the multiple-minima problem in protein folding. In P. M. Pardalos, D. Shalloway, and G. Xue, eds., Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 23. Providence, RI: American Mathematical Society.
9. Li, Y. (1997). Directed annealing search in constraint satisfaction and optimisation, Dissertation, IC-Parc, Imperial College, London.
10. Prestwich, S. (1993). ElipSys programming tutorial, Technical Report ECRC-93-2, ECRC, Munich.
11. Schulze-Kremer, S. (1995). Molecular Bioinformatics: Algorithms and Applications. Walter de Gruyter.
12. Zupanič, D., Hodošček, M., Lavrač, N., & Mozetič, I. (1997). Global energy minimization of small molecules combining constraint logic programming and molecular mechanic. Journal of Chemical Information and Computer Sciences, 37(6): 966-970.