Query language for protein molecular structures

Dominika Wieczorek, Bożena Małysiak-Mrozek, Dariusz Mrozek


Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g. at the level of the SQL language, the structural similarity searching is usually performed by external tools. In the paper, we present our newly developed PSS-SQL language, which allows searching the database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query. Therefore, we provide a simple and declarative language for protein structure similarity searching.


bioinformatics; proteins; secondary structure; similarity

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DOI: http://dx.doi.org/10.21936/si2010_v31.n2A.369