Lattice and off-lattice side chain models of protein folding (extended abstract)

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Lattice and off-lattice side chain models of protein folding (extended abstract): linear time structure prediction better than 86% of optimal

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Annual Conference on Research in Computational Molecular Biology archive
Proceedings of the first annual international conference on Computational molecular biology table of contents

Santa Fe, New Mexico, United States

Pages: 137 - 146

Year of Publication: 1997

ISBN:0-89791-882-7

Authors

William E. Hart	Sandia National Laboratories, Algorithms and Discrete Mathematics Department, P.O. Box 5800, Albuquerque, NM
Sorin Istrail	Sandia National Laboratories, Algorithms and Discrete Mathematics Department, P.O. Box 5800, Albuquerque, NM

Sponsors

SIGACT: ACM Special Interest Group on Algorithms and Computation Theory
DOE : Department of Energy

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ACM New York, NY, USA

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Downloads (6 Weeks): 3, Downloads (12 Months): 26, Citation Count: 4

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REFERENCES

Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.

	1	Richa Agarwala , Serafim Batzoglou , Vlado Dančík , Scott E. Decatur , Martin Farach , Sridhar Hannenhalli , S. Muthukrishnan , Steven Skiena, Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model, Proceedings of the first annual international conference on Computational molecular biology, p.1-2, January 20-23, 1997, Santa Fe, New Mexico, United States [doi>10.1145/267521.267522]
	2	J. E. Atkins, W. E. Hart, and S. Istrail. On the tradeoff between physical accuracy and computational in tractability in protein folding. In STOG 97, 1997. (submitted).
	3	S. Bromberg and K. A. Dill. Side chain entropy and packing in proteins. Prot. Sci., pages 997-1009, 1994.
	4	V. Dan~k and S. Hannenhalli. Protein folding on a triangular mesh, May 1996. Unpublished research.
	5	K. A. Dill. Theory for the folding and stability of globulax proteins. Biochemistry, 24:1501, 1985.
	6	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.
	7	Michael R. Garey , David S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness, W. H. Freeman & Co., New York, NY, 1979
	8	William E. Hart , Sorin Istrail, Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal, Proceedings of the twenty-seventh annual ACM symposium on Theory of computing, p.157-168, May 29-June 01, 1995, Las Vegas, Nevada, United States [doi>10.1145/225058.225106]
	9	William E. Hart , Sorin Istrail, Invariant Patterns in Crystal Lattices: Implications for Protein Folding Algorithms (Extended Abstract), Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching, p.288-303, June 10-12, 1996
	10	W. E. Hart and S. Istrail. Robust proofs of NP-hardness for protein folding: General lattices and energy potentiaJs. J. Comp. Bio., 1996. (submitted).
	11	K. F. Lau and K. A. Dill. A lattice statistical mechanics model of the conformation and sequence spaces of proteins. Macromolecules, 22:3986-3997, 1989.
	12	I. T. Ngo, J. Marks, and M. Karplus. ComputationaJ 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.

CITED BY 4

	Bonnie Berger , Tom Leighton, Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete, Proceedings of the second annual international conference on Computational molecular biology, p.30-39, March 22-25, 1998, New York, New York, United States
	Volker Heun, Approximate protein folding in the HP side chain model on extended cubic lattices, Discrete Applied Mathematics, v.127 n.1, p.163-177, April 2003
	Hans-Joachim Böckenhauer , Dirk Bongartz, Protein folding in the HP model on grid lattices with diagonals, Discrete Applied Mathematics, v.155 n.2, p.230-256, January, 2007
	Abdur Rahman , Albert Y. Zomaya, An overview of protein-folding techniques: issues and perspectives, International Journal of Bioinformatics Research and Applications, v.1 n.1, p.121-143, April 2005