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Items tagged with "chemoinformatics" (9)

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Workflows (7)
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

Tags (7):

Original Uploader

Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 65 times | Downloaded: 26 times

Tags (22):

Original Uploader

Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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 structu...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 85 times | Downloaded: 23 times

Tags (22):

Original Uploader

Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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: 40 times | Downloaded: 17 times

Tags (24):

Original Uploader

Workflow Indigo-pains (1)

Created: 07/06/11 @ 00:39:29 | Last updated: 08/08/11 @ 11:08:04

Credits: User sauberns

Attributions: Workflow RDKit-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. Implementation of the PAINS filters[1] using the Indigo (1.0.0.0000951) nodes in KNIME (2.3.4). 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. The Indigo nodes require installation of the...

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

Viewed: 161 times | Downloaded: 94 times

Tags (7):

Original Uploader

Workflow RDKit-pains-parallel (1)

Created: 13/10/11 @ 02:33:12 | Last updated: 10/08/12 @ 04:56:57

Credits: User sauberns

Attributions: Workflow RDKit-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 (2.0.0.1088) nodes in KNIME (2.5.0). Parallel processing nodes added to take advantage of mutil-core processors. 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 ...

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

Viewed: 43 times | Downloaded: 15 times

Tags (7):

Original Uploader

Workflow RDKit-bioisosteres (1)

Created: 18/01/12 @ 03:42:13 | Last updated: 18/01/12 @ 22:42:28

Credits: User sauberns

Attributions: Workflow RDKit-pains

License: Creative Commons Attribution 3.0 Unported License

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Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

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

Viewed: 81 times | Downloaded: 42 times

Tags (5):

Packs (2)

Pack useful_for_sysmo


Created: 17/12/08 @ 12:31:48 | Last updated: 10/06/09 @ 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

0 items in this pack

Comments: 0 | Viewed: 176 times | Downloaded: 27 times

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Creator

Pack 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...

0 items in this pack

Comments: 0 | Viewed: 45 times | Downloaded: 22 times

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