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Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling Read chapter Read first chapter

2014 | OriginalPaper | Chapter

2. Multithreaded PSS-SQL for Searching Databases of Secondary Structures

Author : Dariusz Mrozek

Published in: High-Performance Computational Solutions in Protein Bioinformatics

Publisher: Springer International Publishing

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Abstract

Protein secondary structure (PSS), as an organizational level, provides important information regarding protein construction and regular spatial shapes, including alpha-helices, beta-strands, and loops, which protein amino acid chain can adopt in some of its regions. The relevance of this information and the scope of its practical applications cause the requirement for its effective storage and processing. In this chapter, we will see how PSSs can be stored in the relational database and processed with the use of the protein secondary structure-structured query language (PSS-SQL). The PSS-SQL is an extension to the SQL language. It allows formulation of queries against a relational database in order to find proteins having secondary structures similar to the structural pattern specified by a user. In this chapter, we will see how this process can be accelerated by parallel implementation of the alignment using multiple threads working on multiple-core CPUs.

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previous chapter Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling
next chapter Parallel CUDA-Based Protein 3D Structure Similarity Searching
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Metadata
Title
Multithreaded PSS-SQL for Searching Databases of Secondary Structures
Author
Dariusz Mrozek
Copyright Year
2014
Book
High-Performance Computational Solutions in Protein Bioinformatics

Print ISBN: 978-3-319-06970-8

Electronic ISBN: 978-3-319-06971-5

Copyright Year: 2014

DOI
https://doi.org/10.1007/978-3-319-06971-5_2

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