On the intractability of protein folding with a finite alphabet of amino acids

Algorithmica (New York)

Volumn 25, Issue 2-3, 1999, Pages 279-294

  Atkins, J ^a   Hart, W E ^b  

^a Tower 45 ^*  (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Intractability; Protein folding; Protein structure prediction

Indexed keywords

EID: 0012363098     PISSN: 01784617     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00008278     Document Type: Article

References (19)

1. R. Agarwala, S. Batzogloa, V. Dančík, S. E. Decatur, S. Hannenhalli, M. Farach, S. Muthukrishnan, and S. Skiena. Local rules for protein folding on a triangular lattice and generalized hydrophobicity. In Proc. RECOMB 97, pages 1-2, 1997.
2. B. Berger and T. Leighton. Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. J. Comput. Biol, 5(1):27-40, 1998.
3. H. S. Chan and K. A. Dill. Comparing folding codes for proteins and polymers. PROTEINS: Structure, Function, and Genetics, 24:335-344, 1996.
4. P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, and M. Yannakakis. On the complexity of protein folding. J. Comput. Biol, 5(3):423-466, 1998.
5. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan. Principles of protein folding: a perspective from simple exact models. Prot. Sci., 4:561-602, 1995.
6. C. J. Epstein, R. F. Goldberger, and C. B. Anfinsen. The genetic control of tertiary protein structure: studies with model systems. In Proc. Cold Spring Harbor Symposium on Quantitative Biology, pages 439-449, 1963.
7. A. S. Fraenkel. Complexity of protein folding. Bull. Math. Biol., 55(6):1199-1210, 1993.
8. M. R. Garey and D. S. Johnson. Computers and Intractability - A Guide to the Theory of NP-completeness. Freeman, San Francisco, CA, 1979.
9. W. E. Hart and S. Istrail. Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. J. Comput. Biol., 3(1):53-96, 1996. Extended abstract in Proc. 27th Annual ACM Symposium on Theory of Computation, May 1995.
10. W. E. Hart and S. Istrail. Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. J. Comput. Biol., 3(1):53-96, 1996. Extended abstract in Proc. 27th Annual ACM Symposium on Theory of Computation, May 1995.
11. W. E. Hart and S. Istrail. Invariant patterns in crystal lattices: implications for protein folding algorithms. In D. Hirshberg and G. Myers, editors, Combinatorial Pattern Matching, pages 288-303. Springer-Verlag, New York, 1996.
12. W. E. Hart and S. Istrail. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal. J. Comput. Biol., 4(3):241-260, 1997. Extended abstract in Proc RECOMB 97, January 1997.
13. W. E. Hart and S. Istrail. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal. J. Comput. Biol., 4(3):241-260, 1997. Extended abstract in Proc RECOMB 97, January 1997.
14. W. E. Hart and S. Istrail. Robust proofs of NP-hardness for protein folding: general lattices and energy potentials. J. Comput. Biol., 4(1):1-20, 1997.
15. A. Nayak, A. Sinclair, and U. Zwick. Spatial codes and the hardness of string folding problems. In Proc Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, pages 639-648, 1998.
16. J. T. Ngo and J. Marks. Computational complexity of a problem in molecular structure prediction. Prot. Engrg., 5(4):313-321, 1992.
17. J. T. Ngo, J. Marks, and M. Karplus. Computational complexity, protein structure prediction, and the Levinthal paradox. In K. Merz, Jr., and S. Le Grand, editors, The Protein Folding Problem and Tertiary Structure Prediction, Chapter 14, pages 435-508. Birkhauser, Boston, MA, 1994.
18. M. Patterson and T. Przytycka. On the complexity of string folding. Discrete Appl. Math., 71:217-230, 1996.
19. R. Unger and J. Moult. Finding the lowest free energy conformation of a protein is a NP-hard problem: proof and implications. Bull. Math. Biol., 55(6):1183-1198, 1993.