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Items tagged with "cdk" (9)

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Workflows (7)

Bioclipse Scripting Language Original Uploader Egon Willighagen	/me is having Bioclipse/XMPP/RDF fun.js (v1) Created: 21/08/09 @ 15:39:04 Credits: 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: 28 times \| Downloaded: 12 times Tags (6): bioclipse \| cdk \| cheminformatics \| chemistry \| dbpedia \| xmpp	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Visualize Molecules from DBPedia as Molecule Table (v3) Created: 14/03/10 @ 20:57:58 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 119 times \| Downloaded: 35 times Tags (7): bioclipse \| cdk \| cheminformatics \| chemistry \| dbpedia \| rdf \| sparql	View Download (v3)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Determine the Maximum Common SubStructure (MCSS) (v1) Created: 23/10/09 @ 12:01:42 Credits: 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: 59 times \| Downloaded: 42 times Tags (3): cdk \| cheminformatics \| mcss	View Download (v1)
Taverna 2 Original Uploader Kalai	Generate Atom Signatures of molecules given SDF as input (v1) Created: 13/05/11 @ 17:14:06 \| Last updated: 13/05/11 @ 19:47:24 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 28 times \| Downloaded: 9 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| synthetic \| taverna 2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v1) Created: 13/05/11 @ 17:22:28 \| Last updated: 13/05/11 @ 17:26:17 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1 Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structural data SM_file:... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 8 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file. - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1 Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 8 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Create a molecules table from a list of IUPAC names (v1) Created: 25/05/11 @ 08:47:34 \| Last updated: 25/05/11 @ 08:47:36 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Scripts that uses OPSIN to convert IUPAC names into chemical structures, which are saved as SD file and openend in the Bioclipse molecules table. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 5 times \| Downloaded: 2 times Tags (7): bioclipse \| cdk \| convert \| iupac name \| mdl sd file \| opsin \| table	View Download (v1)

Packs (1)

Creator:

Kalai

Natural product likeness filter

Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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