Workflows

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Tag: cheminformatics

Workflow Visualize Molecules from DBPedia as Molecu... (3)

Created: 14/03/10 @ 20:57:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 179 times | Downloaded: 46 times

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Workflow Open PDB entries in Jmol for hits found fo... (3)

Created: 14/03/10 @ 21:26:05 | Last updated: 01/03/13 @ 14:37:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Rating: 1.3 / 5 (3 ratings) | Versions: 3 | Reviews: 2 | Comments: 0 | Citations: 0

Viewed: 165 times | Downloaded: 34 times

Tags (10):

Workflow Download CAS numbers and save as SD file (1)

Created: 15/10/09 @ 09:05:39

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 88 times | Downloaded: 65 times

Tags (5):

Workflow Create Ugi Library 001 (1)

Created: 04/12/08 @ 20:34:13

Credits: User Jean-Claude Bradley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Creates a virtual library of SMILES codes for all possible combinations of Ugi products based on lists of SMILES of starting materials in a Google Spreadsheet.  Uses Rajarshi Guha's web service. Can someone create a Taverna workflow that does this?

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 88 times | Downloaded: 52 times

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Workflow Download QSAR data sets using the OpenTox ... (1)

Created: 22/03/10 @ 11:10:25

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Bioclipse script that uses the OpenTox API 1.1 to download all QSAR data sets from a given service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 41 times | Downloaded: 37 times

Tags (5):

Workflow Kabsch Alignment of Small Molecules (1)

Created: 30/10/09 @ 22:12:57

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Aligns molecules using the Kabsch alignment and visualizes the results in the Jmol viewer.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 76 times | Downloaded: 48 times

Tags (5):

Workflow /me is having Bioclipse/XMPP/RDF fun.js (1)

Created: 21/08/09 @ 15:39:04

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioclipse script that combines RDF (DBPedia), XMPP cloud services, and local CDK functionality to gain some information on Farnesol in Bioclipse.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 18 times

Tags (6):

Workflow Determine the Maximum Common SubStructure ... (1)

Created: 23/10/09 @ 12:01:42

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

BSL script to determine the maximum common substructure (MCSS) of a list of molecules and opens this in a JChemPaint editor.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 62 times | Downloaded: 47 times

Tags (3):

Original Uploader

Workflow RDKit-pains (3)

Created: 07/02/11 @ 02:05:36 | Last updated: 08/08/11 @ 11:11:40

Credits: User sauberns

Attributions: Workflow Indigo-pains

License: Creative Commons Attribution 3.0 Unported License

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 If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflow Indigo-pains. Implementation of the PAINS filters[1] using the RDKit (1.0.0.0000763) nodes in KNIME (2.3.1). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with a 10k reference structure set from WEHI[1] which is used by default as input if no other file is chosen. T...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 236 times | Downloaded: 90 times

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