Abstract
3D protein structure similarity searching is one of the most popular processes performed in the structural bioinformatics. The process is usually performed through dedicated websites or desktop software tools, which makes a secondary processing of the search results difficult. One of the alternatives is to store macromolecular data in relational databases and perform the similarity searching on the server-side of the client-server architecture. Unfortunately, relational database management systems (DBMSs) are not designed for efficient storage and processing of biological data, such as 3D protein structures. In this paper, we present the P3D-SQL extension to the Oracle PL/SQL language that allows invoking protein similarity searching in SQL queries and perform the process efficiently against a database of 3D protein structures. Availability: P3D-SQL is available from P3D-SQL project home page at: http://zti.polsl.pl/w3/dmrozek/science/p3dsql.htm
This is a preview of subscription content, log in via an institution to check access.
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
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al.: The Protein Data Bank. Nucleic Acids Res 28, 235–242 (2000)
BioSQL (accessed on January 13, 2015), http://biosql.org/
Date, C.: An introduction to database systems, 8th edn. Addison-Wesley, USA (2003)
Hammel, L., Patel, J.M.: Searching on the secondary structure of protein sequences. In: 28th International Conference on Very Large Data Bases, VLDB 2002, pp. 634—645, Hong Kong, China (2002)
Kwon, T., Chang, J.H., Kwak, E., Lee, C.W., et al.: Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet. EMBO J 22, 292–303 (2003), http://dx.doi.org/10.1093/emboj/cdg025
Mrozek, D., Socha, B., Kozielski, S., Małysiak-Mrozek, B.: An efficient and flexible scanning of databases of protein secondary structures with the segment index and multithreaded alignment. J. Intell. Inf. Syst. (in press), http://dx.doi.org/10.1007/s10844-014-0353-0
Mrozek, D., Wieczorek, D., Małysiak-Mrozek, B., Kozielski, S.: PSS-SQL: Protein Secondary Structure - Structured Query Language. In: 32th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2010, Buenos Aires, Argentina, vol. 2010, pp. 1073–1076 (2010)
Prlic, A., et al.: BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28, 2693–2695 (2012)
Shindyalov, I., Bourne, P.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 11(9), 739–747 (1998)
Stephens, S.M., Chen, J.Y., Davidson, M.G., Thomas, S., Trute, B.M.: Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. Nucl. Acids Res. 33(suppl. 1), D675-D679 (2005), http://dx.doi.org/10.1093/nar/gki114
Tata, S., Friedman, J.S., Swaroop, A.: Declarative querying for biological sequences. In: 22nd International Conference on Data Engineering, pp. 87–98. IEEE Computer Society, Atlanta (2006)
Westbrook, J., Fitzgerald, P.: The PDB format, mmCIF, and other data formats. Methods Biochem Anal 44, 161–179 (2003)
Ye, Y., Godzik, A.: Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19(2), 246–255 (2003)
Zhu, G., Liu, J., Terzyan, S., Zhai, P., Li, G., Zhang, X.C.: High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop. J. Biol. Chem. 278, 2452–2460 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Mrozek, D., Małysiak-Mrozek, B., Adamek, R. (2015). P3D-SQL: Extending Oracle PL/SQL Capabilities Towards 3D Protein Structure Similarity Searching. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9043. Springer, Cham. https://doi.org/10.1007/978-3-319-16483-0_53
Download citation
DOI: https://doi.org/10.1007/978-3-319-16483-0_53
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-16482-3
Online ISBN: 978-3-319-16483-0
eBook Packages: Computer ScienceComputer Science (R0)