Abstract
In this paper, we present a novel approximation algorithm to solve the protein folding problem in the H-P model. Our algorithm is polynomial in terms of the length of the given H-P string. The expected approximation ratio of our algorithm is \(1- \dfrac{2\log n }{n-1}\) for n ≥ 6, where n 2 is the total number of H in a given H-P string. The expected approximation ratio tends to 1 for large values of n. Hence our algorithm is expected to perform very well for larger H-P strings.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Agarwala, R., Batzoglou, S., Dancík, V., Decatur, S.E., Hannenhalli, S., Farach, M., Muthukrishnan, S., Skiena, S.: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the hp model. Journal of Computational Biology 4(3), 275–296 (1997)
Dill, K.A.: Theory for the folding and stability of globular-proteins. Biochemistry 24(6), 1501–1509 (1985)
Hart, W.E., Istrail, S.: Fast protein folding in the hydrophobic-hydrophillic model within three-eights of optimal. Journal of Computational Biology 3(1), 53–96 (1996)
Hart, W.E., Istrail, S.: Invariant patterns in crystal lattices: Implications for protein folding algorithms (extended abstract). In: Hirschberg, D.S., Meyers, G. (eds.) CPM 1996. LNCS, vol. 1075, pp. 288–303. Springer, Heidelberg (1996)
Hart, W.E., Istrail, S.: Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal. Journal of Computational Biology 4(3), 241–259 (1997)
Heun, V.: Approximate protein folding in the HP side chain model on extended cubic lattices (Extended abstract). In: Nešetřil, J. (ed.) ESA 1999. LNCS, vol. 1643, pp. 212–223. Springer, Heidelberg (1999)
Istrail, S., Lam, F.: Combinatorial algorithms for protein folding in lattice models: A survey of mathematical results. Communications in Information and Systems 9(4), 303–346 (2009)
Jiang, M., Zhu, B.: Protein folding on the hexagonal lattice in the hp model. J. Bioinformatics and Computational Biology 3(1), 19–34 (2005)
Kessler, I., Livingston, M.: The expected number of parts in a partition of n. Monatshefte für Mathematik 81(3), 203–212 (1976)
Newman, A.: A new algorithm for protein folding in the hp model. In: SODA, pp. 876–884 (2002)
Newman, A., Ruhl, M.: Combinatorial problems on strings with applications to protein folding. In: Farach-Colton, M. (ed.) LATIN 2004. LNCS, vol. 2976, pp. 369–378. Springer, Heidelberg (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Islam, A.S.M.S., Rahman, M.S. (2013). Protein Folding in 2D-Triangular Lattice Revisited. In: Lecroq, T., Mouchard, L. (eds) Combinatorial Algorithms. IWOCA 2013. Lecture Notes in Computer Science, vol 8288. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45278-9_21
Download citation
DOI: https://doi.org/10.1007/978-3-642-45278-9_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-45277-2
Online ISBN: 978-3-642-45278-9
eBook Packages: Computer ScienceComputer Science (R0)