Abstract
Mining for common motifs in protein tertiary structures holds the key to the understanding of protein functions. However, due to the formidable problem size, existing techniques for finding common substructures are computationally feasible only under certain artificially imposed constraints, such as using super-secondary structures and fixed-length segmentation. This paper presents the first, pure tertiary-level algorithm that discovers the common protein substructures without such limitations. Modeling this as a maximal common subgraph (MCS) problem, the solution is found by further mapping into the domain of maximum clique (MC). Coupling a MC solver with a graph coloring (GC) solver, the iterative algorithm, CRP-GM, is developed to narrow down towards the desired solution by feeding results from one solver into the other. The solution quality of CRP-GM amply demonstrates its potential as a new and practical data-mining tool for molecular biologists, as well as several other similar problems requiring identification of common substructures.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Jones, T.A., Thirup, S.: Using Known Substructures in Protein Model Building and Crystallography. EMBO J. 5(4), 819–822 (1986)
Vriend, G., Sander, C.: Detection of common three-dimensional substructures in proteins. Proteins 11, 52–58 (1991)
Grindley, H.M., Artymiuk, P.J., Rice, D.W., Willett, P.: Identification of Tertiary Structure Resemblance in Proteins Using a Maximal Common Subgraph Isomorphism Algorithm. J. Mol. Biol. 229, 707–721 (1993)
Holm, L., Sander, C.: Protein Structure Comparison by Alignment of Distance Matrices. J. Mol. Biol. 233, 123–138 (1993)
Brint, A.T., Willett, P.: Algorithms for the Identification of Three-dimensional Maximal Common Substructures. J. Chem. Inform. Comput. Sci. 27, 152–158 (1987)
Barrow, H.G., Burstall, R.M.: Subgraph Isomorphism, Matching Relational Structures and Maximal Cliques. Information Processing Letters 4, 83–94 (1976)
C.-w. Chen, Algorithms for Maximal Common Subgraph Problem Using Resource Planning, Ph.D. Dissertation, University of Hawaii (1999)
Bollbas, B.: Extermal Graph Theory. Academic Press, London (1978)
Kent, N.P., Yun, D.Y.Y.: A Planning/Scheduling Methodology for the Constrained Resource Problem. In: Proceedings of the Eleventh International Joint Conference on Artificial Intelligence, pp. 20–25 (1989)
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
Chen, Cw.K., Yun, D.Y.Y. (1999). Knowledge Discovery for Protein Tertiary Substructures. In: Zhong, N., Skowron, A., Ohsuga, S. (eds) New Directions in Rough Sets, Data Mining, and Granular-Soft Computing. RSFDGrC 1999. Lecture Notes in Computer Science(), vol 1711. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-48061-7_52
Download citation
DOI: https://doi.org/10.1007/978-3-540-48061-7_52
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-66645-5
Online ISBN: 978-3-540-48061-7
eBook Packages: Springer Book Archive