Abstract
One of the most important open problems in computational molecular biology is the prediction of the conformation of a protein based on its amino acid sequence. In this paper, we design approximation algorithms for structure prediction in the so-called HP side chain model. The major drawback of the standard HP side chain model is the bipartiteness of the cubic lattice. To eliminate this drawback, we introduce the extended cubic lattice which extends the cubic lattice by diagonals in the plane. For this lattice, we present two linear algorithms with approximation ratios of 59/70 and 37/42, respectively. The second algorithm is designed for a ‘natural’ subclass of proteins, which covers more than 99:5% of all sequenced proteins. This is the first time that a protein structure prediction algorithm is designed for a ‘natural’ subclass of all combinatorially possible sequences.
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
R. Agarwala, S. Batzoglou, V. Dančík, S. Decatur, M. Farach, S. Hannenhalli, S. Muthukrishnan, S. Skiena: Local Rules for Protein Folding on a Triangular Lattice and generalized Hydrophobicity in the HP Model, Proceedings of the 8th Symposium on Discrete Algorithms, 390–399, 1997, also in Proceedings of the First Conference on Computational Molecular Biology, 1-2, 1997.
B. Berger, F. T. Leighton: Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete, Proceedings of the 2nd Conference on Computational Molecular Biology, 30–39, 1998.
P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis: On the Complexity of Protein Folding, Proceedings of the 30th Symposium on Theory of Computing, 597–603, 1998, also in Proceedings of the 2nd Conference on Computational Molecular Biology, 61-62, 1998.
K. A. Dill: Dominant Forces in Protein Folding, Biochemistry, 29(31):7133–7155, 1990.
K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. Yee, P. Thomas, H. Chan: Principles of Protein Folding: A Perspective From Simple Exact Models, Prot. Sci., 4:561–602, 1995.
A. Fraenkel: Complexity of Protein Folding, Bull. Math. Biol., 55(6):1199–1210, 1993.
W. E. Hart, S. Istrail: Fast Protein Folding in the Hydrophobic-Hydrophilic Model Within Three-Eights of Optimal, Proceedings of the 27th Symposium on Theory of Computing, 157–167, 1995.
W. E. Hart, S. Istrail: Fast Protein Folding in the Hydrophobic-Hydrophilic Model Within Three-Eights of Optimal, J. Comp. Biol., 3(1):53–96, 1996.
W. E. Hart, S. Istrail: Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better Than 86% of Optimal, Proceedings of the 2nd Conference on Computational Molecular Biology, 137–146, 1997.
A. Nayak, A. Sinclair, U. Zwick: Spatial Codes and the Hardness of String Folding Problems, Proceedings of the 9th Symposium on Discrete Algorithms, 639–648, 1998.
J. T. Ngo, J. Marks: Computational Complexity of a Problem in Molecular Structure Prediction, Prot. Engng., 5(4):313–321, 1992.
J. T. Ngo, J. Marks, M. Karplus: Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox, in The Protein Folding Problem and Tertiary Structure Prediction, K. Merz Jr., S. LeGrand (Eds.), Birkhäuser, 1994.
M. Paterson, T. Przytycka: On the Complexity of String Folding, Proceedings of the 23rd Int’l Colloquium on Automata, Languages, and Programming, 658–669, 1996.
S. Sun, R. Brem, H. D. Chan, K. A. Dill: Designing Amino Acid Sequences to Fold with Good Hydrophobic Cores, Prot. Engng. 8(12):1205–1213, 1995.
R. Unger, J. Moult: Finding the Lowest Free Energy Conformation of a Protein is an NP-Hard Problem: Proof and Implications, Bull. Math. Biol., 55(6):1183–1198, 1993.
SWISS-PROT Protein Sequence Data Bank: http://www.expasy.ch/sprot/, ftp://www.expasy.ch/databases/swiss-prot/sprot36.dat (as of July 21, 1998).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Heun, V. (1999). Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices (Extended Abstract). In: Nešetřil, J. (eds) Algorithms - ESA’ 99. ESA 1999. Lecture Notes in Computer Science, vol 1643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48481-7_19
Download citation
DOI: https://doi.org/10.1007/3-540-48481-7_19
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-66251-8
Online ISBN: 978-3-540-48481-3
eBook Packages: Springer Book Archive