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

SEHNAL, David, Lukáš PRAVDA, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU and Jaroslav KOČA. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Research. Oxford: Oxford University Press, 2015, vol. 43, W1, p. "W383"-"W388", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv561.

Basic information

• Original name: PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank
• Authors: SEHNAL, David (203 Czech Republic, belonging to the institution), Lukáš PRAVDA (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Crina-Maria IONESCU (642 Romania, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution).
• Edition: Nucleic Acids Research, Oxford, Oxford University Press, 2015, 0305-1048.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 9.202
• RIV identification code: RIV/00216224:14740/15:00082987
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1093/nar/gkv561
• UT WoS: 000359772700060
• Keywords in English: protein structure; protein structural pattern; structural bioinformatics; Protein Data Bank; query language
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

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.

Links

• ED1.1.00/02.0068, research and development project: Name: CEITEC - central european institute of technology
• EE2.3.30.0009, research and development project: Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci
• LH13055, research and development project: Name: Multidisciplinární přístup k návrhu léčiv - Inhibice proteinů s návazností na cukry (Acronym: MADICA)

Investor: Ministry of Education, Youth and Sports of the CR

• MUNI/A/0855/2013, interní kód MU: Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace III. (Acronym: FI MAV III.)

Investor: Masaryk University, Category A

• MUNI/A/1159/2014, interní kód MU: Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IV.

Investor: Masaryk University, Category A