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

Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J - Nucleic Acids Res. (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic.

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The query recognizes the binding pocket of any residue containing a pyranose moiety in the envelope glycoprotein gp160 from Human immunodeficiency virus 1 in complex with Homo sapiens immunoglobulins (3u7y). One of the recognized patterns is highlighted in the box. (A) First, the query identifies a pyranose moiety (a ring composed of 5 carbons and an oxygen atom). (B) Then, all residues which include this pattern in their structure are identified. (C) Finally, all the residues that are at most 4Å from any of the pyranose containing residues are detected as well. This ensures all the potential coordination partners are recognized properly. The molecules were visualized using PyMOL.
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Figure 1: The query recognizes the binding pocket of any residue containing a pyranose moiety in the envelope glycoprotein gp160 from Human immunodeficiency virus 1 in complex with Homo sapiens immunoglobulins (3u7y). One of the recognized patterns is highlighted in the box. (A) First, the query identifies a pyranose moiety (a ring composed of 5 carbons and an oxygen atom). (B) Then, all residues which include this pattern in their structure are identified. (C) Finally, all the residues that are at most 4Å from any of the pyranose containing residues are detected as well. This ensures all the potential coordination partners are recognized properly. The molecules were visualized using PyMOL.

Mentions: PatternQuery is an interactive web application for the optimal definition of biomacromolecular structural patterns, followed by their fast detection and extraction from the entire PDB or user defined datasets. These patterns are described by unique expressions based on the Python programming language, which are designed to define biomacromolecular structural patterns based on the nature and relationship between atoms, residues and other structural elements. These expressions define the composition, topology, connectivity, and 3D structure of a pattern. By composing these expressions into a query, 3D structural patterns can be identified inside biomacromolecules. Figure 1 gives the PQ query example that identifies and extracts a 3D pattern made up of a residue containing a pyranose moiety, together with its immediate surroundings.


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

Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J - Nucleic Acids Res. (2015)

The query recognizes the binding pocket of any residue containing a pyranose moiety in the envelope glycoprotein gp160 from Human immunodeficiency virus 1 in complex with Homo sapiens immunoglobulins (3u7y). One of the recognized patterns is highlighted in the box. (A) First, the query identifies a pyranose moiety (a ring composed of 5 carbons and an oxygen atom). (B) Then, all residues which include this pattern in their structure are identified. (C) Finally, all the residues that are at most 4Å from any of the pyranose containing residues are detected as well. This ensures all the potential coordination partners are recognized properly. The molecules were visualized using PyMOL.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489247&req=5

Figure 1: The query recognizes the binding pocket of any residue containing a pyranose moiety in the envelope glycoprotein gp160 from Human immunodeficiency virus 1 in complex with Homo sapiens immunoglobulins (3u7y). One of the recognized patterns is highlighted in the box. (A) First, the query identifies a pyranose moiety (a ring composed of 5 carbons and an oxygen atom). (B) Then, all residues which include this pattern in their structure are identified. (C) Finally, all the residues that are at most 4Å from any of the pyranose containing residues are detected as well. This ensures all the potential coordination partners are recognized properly. The molecules were visualized using PyMOL.
Mentions: PatternQuery is an interactive web application for the optimal definition of biomacromolecular structural patterns, followed by their fast detection and extraction from the entire PDB or user defined datasets. These patterns are described by unique expressions based on the Python programming language, which are designed to define biomacromolecular structural patterns based on the nature and relationship between atoms, residues and other structural elements. These expressions define the composition, topology, connectivity, and 3D structure of a pattern. By composing these expressions into a query, 3D structural patterns can be identified inside biomacromolecules. Figure 1 gives the PQ query example that identifies and extracts a 3D pattern made up of a residue containing a pyranose moiety, together with its immediate surroundings.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic.

Show MeSH
Related in: MedlinePlus