A Method of Structure Comparison Using Spatial Topological Patterns


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The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.



Key Engineering Materials (Volumes 277-279)

Edited by:

Kwang Hwa Chung, Yong Hyeon Shin, Sue-Nie Park, Hyun Sook Cho, Soon-Ae Yoo, Byung Joo Min, Hyo-Suk Lim and Kyung Hwa Yoo




S. H. Park and K. H. Ryu, "A Method of Structure Comparison Using Spatial Topological Patterns", Key Engineering Materials, Vols. 277-279, pp. 272-277, 2005

Online since:

January 2005




[1] S. H. Park, K. H. Ryu, H. S. Son, Modeling Protein Structures with Spatial Model for Structure Comparison, IDEAL 03', LNCS 2690, pp.490-497, Springer-Verlag Berlin Heidelberg, (2003).

[2] Orhan Camoglu, Tamer Kahveci, and Ambuj K. Singh, PSI: indexing protein structures for fast similarity search, Bioinformatics 2003 19: 81i-83i.

DOI: https://doi.org/10.1093/bioinformatics/btg1009

[3] Oracle Spatial User's Guide and Reference: Loading and Indexing Spatial Object Types. Release 8. 1. 5, Oracle (2001).

[4] Holm L, Park J, DaliLite workbench for protein structure comparison, Bioinformatics 2000, 16(6): 566-567.

DOI: https://doi.org/10.1093/bioinformatics/16.6.566

[5] C.A. Orengo and W.R. Taylor, SSAP: sequential structure alignment program for protein structure comparison, Methods in Enzymology, 266, 1996, p.617. 635.

DOI: https://doi.org/10.1016/s0076-6879(96)66038-8

[6] L. Holm, C. Sander: Proein structure comparison by alignment of distance matrices, Journal of Molecular Biology, 233, 1993, pp.123-138.

[7] E. Clementini, P. Felice, P. van Oostrom: A small set of formal topological relationships suitable for end-user interaction. In: Proc. of Spatial Databases Symp., Singapore (1993) 277-295.

DOI: https://doi.org/10.1007/3-540-56869-7_16

[8] Amit P. Singh, Douglas L. Brutlag: Protein Structure Alignment: A Comparison of Methods, Dept. of Biochemistry, Stanford Univ, CA, (2000).

[9] J-F. Gibrat, T. Madej, and H. Bryant, Surprising similarities in structure comparison, Current Opinion in Structural Biology, 6, 1996, pp.377-385.

DOI: https://doi.org/10.1016/s0959-440x(96)80058-3

[10] A. Martin, The ups and downs of protein topology: rapid comparison of protein structure, Protein Engineering, 13, 2000, pp.829-837.

DOI: https://doi.org/10.1093/protein/13.12.829

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