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Tag: structure retrieval

Workflow Structure_or_ID (1)

Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output.

Created: 2008-06-06

Credits: User Hamish McWilliam

Workflow EBI_dbfetch_fetchBatch (1)

Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.

Created: 2009-08-28

Credits: User Hamish McWilliam

Workflow dbfetch tutorial (1)

This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is alw...

Created: 2008-09-22

Credits: User Steffen Möller


Workflow Download Structures from PubChem given che... (1)

This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

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