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PatternQuery specifications

Information


Unique identifier OMICS_08685
Name PatternQuery
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jaroslav Koča

Publication for PatternQuery

PatternQuery citations

 (3)
library_books

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL

2017
PLoS One
PMCID: 5726637
PMID: 29232414
DOI: 10.1371/journal.pone.0189375

[…] e Trp side chain conformation found in these complexes. The PDB database was searched to find all binding sites with sugar ligands that are bound by CH-π stacking interaction with tryptophan. We used PatternQuery program for searching.[] The sugar ligand was defined as a ligand that contains a five or six membered ring with single bonds only, which contains one oxygen atom and four or five carbon […]

library_books

Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes

2017
Sci Rep
PMCID: 5651878
PMID: 29057979
DOI: 10.1038/s41598-017-13990-0

[…] ‘constellations’ for ene-reductase activity, use of BioGPS descriptors to aid discovery of promiscuous side-activity or the retrieval of catalytic residue arrangements via the Catalytic Site Atlas or PatternQuery,. Whilst these methods provide simple means of accessing proteins with desired catalytic activity, their use is mostly limited to structural databases containing only a fraction of the nu […]

library_books

The Eighth Central European Conference “Chemistry towards Biology”: Snapshot†

2016
PMCID: 5283649
PMID: 27763518
DOI: 10.3390/molecules21101381

[…] PDBsum integrates ligand validation results from ValidatorDB and information about channels, precalculated via MOLE. Protein Data Bank Europe includes a Coordinate Server [], which is based on PatternQuery and enables the user to extract predefined parts of the PDB entry (e.g., backbone, selected residues, etc.). […]

Citations

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PatternQuery institution(s)
CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic

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