The number of known proteins is increasing every day; tens of thousands have been studied and categorized by now.
In this chapter, we propose a model for protein matching or extracting similar parts of two given proteins. We focus on the computational geometric approach and the graph matching method that are used to model and compare the sequence and 3D structure of proteins.
The remainder of this chapter is organized as follows. We first have a glance at the related works. There are two major methods used in the literature: Delaunay tetrahedralization and similarity flooding.We explain the required information in the next section as background knowledge, and then propose a new idea in Sect. 33.4 which can improve the current methods.We then present experimental results of the implemented method which show its effectiveness.
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References
Eidhammer I, Jonasses I, Taylor W (2000) Structure comparison and structure patterns. Journal of Computational Biology. Volume 7. 685–716
Finney J (1970) Random packing and the structure of simple liquids, the geometry of the random close packing. Proceedings of the Royal Society. Volume 319. 479–493
Tropsha A, Carter C, Cammer S, Vaisman I (2003) Simplicial neighborhood analysis of protein packing (SNAPP): A computational geometry approach to studying proteins. Methods in Enzymology. Volume 374. 509–544
Cho W Z S, Vaisman I, Tropsha A (1997) A new approach to protein fold recognition based on delaunay tessellation of protein structure. In: Pacific Symposium on Biocomputing, Singapore 487–496
Carter C, LeFebvre B, Cammer S, Trosha A, Edgell M (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. Journal of Molecular Biology. Volume 311. No. 4. 625–638
Roach J, Sharma S, Kapustina M, Carter C (2005) Structure alignment via delaunay tetrahedralization. Proteins: Structure, Function, and Bioinformatics. Volume 60. 66–81
Bostick D, Shen M, Vaisman I (2004) A simple topological representation of protein structure: Implications for new, fast, and robust structural classification. Proteins: Structure, Function, and Bioinformatics. Volume 56. 487–501
Hun J, Bandyopadhyay D, Wang W, Snoeyink J, Prins J, Trosha A (2005) Comparing graph representations of protein structure for mining family-specific residue-based packing motifs. Journal of Computational Biology. Volume 12. 657–671
Dafas P, Gomoluch A K, Schroeder M (2004) Structural protein interactions: From months to minutes. In: Elsevier B.V, Parallel Computing: Software Technology, Algorithms, Architectures & Applications. 677–684
Park J, Lappe M, Teichmann S A (2001) Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Journal of Molecular Biology. Volume 307. No. 3. 929–938
Garcia-Molina S M H, Rahm E (2002) Similarity flooding: A versatile graph matching algorithm and its application to schema matching. In: Proceedings of the 18th International Conference on Data Engineering (ICDE), San Jose, CA
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Sayyadi, H., Salehi, S., Ghodsi, M. (2008). SimDiv: A New Solution for Protein Comparison. In: Castillo, O., Xu, L., Ao, SI. (eds) Trends in Intelligent Systems and Computer Engineering. Lecture Notes in Electrical Engineering, vol 6. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74935-8_33
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DOI: https://doi.org/10.1007/978-0-387-74935-8_33
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