Informace o publikaci

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

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SEHNAL David PRAVDA Lukáš SVOBODOVÁ VAŘEKOVÁ Radka IONESCU Crina-Maria KOČA Jaroslav

Rok publikování 2015
Druh Článek v odborném periodiku
Časopis / Zdroj Nucleic Acids Research
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://dx.doi.org/10.1093/nar/gkv561
Doi http://dx.doi.org/10.1093/nar/gkv561
Obor Biochemie
Klíčová slova protein structure; protein structural pattern; structural bioinformatics; Protein Data Bank; query language
Popis Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
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