Multithreaded PSS-SQL for searching databases of secondary structures

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.