title: PSS-SQL: protein secondary structure - structured query language.
abstract: 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 a 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.
authors.affiliation: Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland. Dariusz.Mrozek@polsl.pl
authors.forename: Dariusz
authors.initials: D
authors.lastname: Mrozek
authors.forename: Dominika
authors.initials: D
authors.lastname: Wieczorek
authors.forename: Bozena
authors.initials: B
authors.lastname: Malysiak-Mrozek
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Kozielski
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011381:Programming Languages; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins