Complexity of protein folding
- Aviezri S. Fraenkel
- … show all 1 hide
Purchase on Springer.com
$39.95 / €34.95 / £29.95*
Rent the article at a discountRent now
* Final gross prices may vary according to local VAT.
It is believed that the native folded three-dimensional conformation of a protein is its lowest free energy state, or one of its lowest. It is shown here that both a two-and three-dimensional mathematical model describing the folding process as a free energy minimization problems is NP-hard. This means that the problem belongs to a large set of computational problems, assumed to be very hard (“conditionally intractable”). Some of the possible ramifications of this results are speculated upon.
Supplementary Material (0)
- Anfinsen, C. B. 1973. Principles that govern the folding of protein chains.Science 181, 223–230.
- Barahona, f. 1982. On the computational complexity of ising spin glass models.J. Phys. A: Math. Gen. 15, 3241–3253. CrossRef
- Barahona, F., R. Maynard, R. Rammal and J. P. Uhry. 1982. Morphology of ground states of two-dimensional frustration model.J. Phys. A: Math. Gen. 15, 673–699. CrossRef
- Baxter, R. J. 1982.Exactly Solved Models in Statistical Mechanics London: Academic Press.
- Bennett, C. H., F. Bessette, G. Brassard, L. Salvail and J. Smolin. 1992a. Experimental quantum cryptographys.J. Crypt. 5, 3–28.
- Bennett, C. H. and G. Brassard. 1989. The dawn of a new era for quantum cryptography: the experimental prototype is working!,Assoc. comput. mach SIGACT News 20 (4), 78–82. CrossRef
- Bennett, C. H., G. Brassard C. Crépeau and M.-H. Skubiszewska. 1992b. Practical quantum oblivious transfer.Proc. Crypt. 91, 351–366.
- Bennett, C. H., G. Brassard and N. D. Mermin. 1992. Quantum cryptography without Bell's theorem.Phys. Rev. Lett. 68. 557–559. CrossRef
- Bieche, I., R. Maynard, R. Rammal and J. P. Uhry. 1980. On the ground states of the frustration model of a spin glass by a matching method of graph theory.J. Phys. A. Math. Gen. 13, 2553–2567. CrossRef
- Brassard, G. 1988.Modern Cryptology, Lecture Notes in Computer Science, Vol. 325. New York: Springer-Verlag.
- Brassard, G. and C. Crépeau. 1990. Quantum bit commitment and coin tossing protocols.Proc. Crypt. 90, 49–61.
- Deutsch, D. 1985. Quantum theory, the Church-Turing principle and the universal quantum computer.Proc. R. Soc. London A 400, 97–117.
- Deutsch, D. 1989. Quantum computational networks.Proc. R. Soc. London A 425, 73–90. CrossRef
- Fraenkel, A. S. 1990. Deexponentializing complex computational mathematical problems using physical or biological systems. Technical Report CS90-30. Department of Applied mathematics and Computer Science. Weizman Institute of Science.
- Garey, M. R. and D. S. Johnson. 1979.Computers and Intractability: A Guide to the Theory of NP-Completeness. San Francisco, CA: Freeman.
- Gierasch, L. M. and J. King (Eds.) 1990.Protein folding: Deciphering the Second Half of the Genetic Code. Washington, D.C.: American Association for the Advacement of Science.
- Janin, J. and S. J. Wodak. 1983. Structural domains in proteins and their role in the dynamics of protein function.Prog. Biophys molec. Biol. 42, 21–78. CrossRef
- Levitt, M. and S. Lifson. 1969. Refinement of protein conformations using a macromolecular energy minimization procedure.J. molec. Biol. 46, 269–279. CrossRef
- Levitt, M. and R. Sharon. 1988. Accurate simulation of protei dynamics in solution.Proc. natn. Acad. Sci. U.S.A. 85, 7557–7561. CrossRef
- Privalov, P. L. 1979. Stability of proteins.Adv. Protein Chem. 33, 167–241.
- Privalov, P. L. 1982. Stability of proteins: proteins which do not present a single cooperative system.Adv. Protein Chem. 35, 1–104. CrossRef
- Robertson, N. and P. D. Seymour. 1988. Graph minors XV, Wagner's conjecture, manuscript.
- Unger, R. and J. Moult. 1993. Finding the lowest free energy conformation of a protein is a NP-complete problem: proof and implications.Bull. math. Biol. 55, 1183–1198. CrossRef
- Wasserman, S. A. and N. R. Cozzarelli. 1986. Biochemical topology: applications to DNA recombination and replication.Science 232, 951–960.
- Welsh, D. J. A. 1993. The complexity of knots.Ann. Disc. Math. 55, 159–171. CrossRef
- Wiesner, S. 1983. Conjugate coding.Assoc. comput. mach. SIGACT News 15 (1), 78–88 (manuscript written about 1970). CrossRef
About this Article
- Complexity of protein folding
Bulletin of Mathematical Biology
Volume 55, Issue 6 , pp 1199-1210
- Cover Date
- Print ISSN
- Online ISSN
- Kluwer Academic Publishers
- Additional Links
- Author Affiliations
- 1. Department of Mathematics, University of Pennsylvania, 19104-6395, Philadelphia, CA, U.S.A.