Další formáty:
BibTeX
LaTeX
RIS
@article{1300113,
author = {Sehnal, David and Pravda, Lukáš and Svobodová Vařeková, Radka and Ionescu, CrinaandMaria and Koča, Jaroslav},
article_location = {Oxford},
article_number = {W1},
doi = {http://dx.doi.org/10.1093/nar/gkv561},
keywords = {protein structure; protein structural pattern; structural bioinformatics; Protein Data Bank; query language},
language = {eng},
issn = {0305-1048},
journal = {Nucleic Acids Research},
title = {PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank},
url = {http://dx.doi.org/10.1093/nar/gkv561},
volume = {43},
year = {2015}
}
TY - JOUR
ID - 1300113
AU - Sehnal, David - Pravda, Lukáš - Svobodová Vařeková, Radka - Ionescu, Crina-Maria - Koča, Jaroslav
PY - 2015
TI - PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank
JF - Nucleic Acids Research
VL - 43
IS - W1
SP - "W383"-"W388"
EP - "W383"-"W388"
PB - Oxford University Press
SN - 03051048
KW - protein structure
KW - protein structural pattern
KW - structural bioinformatics
KW - Protein Data Bank
KW - query language
UR - http://dx.doi.org/10.1093/nar/gkv561
L2 - http://dx.doi.org/10.1093/nar/gkv561
N2 - 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.
ER -
SEHNAL, David, Lukáš PRAVDA, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU a Jaroslav KOČA. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2015, roč.~43, W1, s.~''W383''-''W388'', 6 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv561.
|
