Robust proofs of NP-Hardness for protein folding: General lattices and energy potentials

Journal of Computational Biology

Volumn 4, Issue 1, 1997, Pages 1-22

  Hart, William E ^a   Istrail, Sorin ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

intractability, robustness, lattice models; protein folding

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; STRUCTURE ANALYSIS;

EID: 0030901866     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1997.4.1     Document Type: Article

References (16)

1. Allen, M.P., and Tildesley, D.J. 1987. Computer Simulation of Liquids. Oxford Science Publications, Oxford.
2. Atkins, J., and Hart, W.E. 1997 (Unpublished research).
3. Bromberg, S., and Dill, K.A. 1994. Side chain entropy and packing in proteins. Prot. Sci. 997-1009.
4. Chan, H.S., and Dill, K.A. 1996. Comparing folding codes for proteins and polymers. PROTEINS: Structure, Function, and Genetics 24, 335-344.
5. Creighton, T.E., ed. 1993. Protein Folding. W.H. Freeman and Co., New York.
6. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., and Chan, H.S. 1995. Principles of protein folding: A perspective from simple exact models. Prot. Sci. 4, 561-602.
7. Epstein, C.J., Goldberger, R.F., and Anfinsen, C.B. 1963. The genetic control of tertiary protein structure: Studies with model systems. In Cold Spring Harbor Symposium on Quantitative Biology, 28, 439-449.
8. Fraenkel, A.S. 1993. Complexity of protein folding. Bull. Math. Biol. 55(6), 1199-1210.
9. Garey, M.R., and Johnson, D.S. 1979. Computers and Intractability - A guide to the theory of NP-completeness. W.H. Freeman and Co., New York.
10. Hart, W.E., and Istrail, S. 1996. Invariant patterns in crystal lattices: Implications for protein folding algorithms (extended abstract). In Proc. 7th Annual Symp. on Combinatorial Pattern Matching, 288-303.
11. Ngo, J.T., and Marks, J. 1992. Computational complexity of a problem in molecular structure prediction. Protein Engineering 5(4), 313-321.
12. Ngo, J.T., Marks, J., and Karplus, M. 1994. Computational complexity, protein structure prediction, and the Levinthal paradox. In K. Merz, Jr. and S. Le Grand, eds. The Protein Folding Problem and Tertiary Structure Prediction, 435-508. Birkhauser, Boston, MA.
13. Patterson, M., and Przytycka, T. 1995. On the complexity of string folding. In Istrail, S., Pevzner, P., and Shamir, R. eds. Discrete Applied Mathematics, Special Issue on Computational Molecular Biology. Vol. 71, No. 1-3, December 1996, pp. 217-230.
14. Unger, R., and Moult, J. 1993. Finding the lowest free energy conformation of a protein is a NP-hard problem: Proof and implications. Bull. Math. Biol. 55(6), 1183-1198
15. van Gunsteren, W.F., Weiner, P.K., and Wilkinson, A.J., eds. 1993. Computer Simulation of Biomolecular Systems. ESCOM Science Publishers, New York.
16. Wells, A.F. 1979. Three-Dimensional Nets and Polyhedra. American Crystallographic Association, New York.