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Items tagged with "chemoinformatics" (9)

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Workflows (7)

KNIME Original Uploader sauberns	RDKit-pains (v3) Created: 07/02/11 @ 02:05:36 \| Last updated: 08/08/11 @ 11:11:40 Credits: sauberns Attributions: Indigo-pains License: Creative Commons Attribution 3.0 Unported License 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: 144 times \| Downloaded: 46 times Tags (7): cheminformatics \| chemoinformatics \| drug development \| hts \| knime \| pains \| rdkit	View Download (v3)
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)
KNIME Original Uploader sauberns	Indigo-pains (v1) Created: 07/06/11 @ 00:39:29 \| Last updated: 08/08/11 @ 11:08:04 Credits: sauberns Attributions: RDKit-pains License: Creative Commons Attribution 3.0 Unported License 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: 80 times \| Downloaded: 50 times Tags (7): cheminformatics \| chemoinformatics \| drug development \| hts \| indigo \| knime \| pains	View Download (v1)
KNIME Original Uploader sauberns	RDKit-pains-parallel (v1) Created: 13/10/11 @ 02:33:12 \| Last updated: 16/12/11 @ 04:05:14 Credits: sauberns Attributions: RDKit-pains License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 11 times \| Downloaded: 1 time Tags (7): cheminformatics \| chemoinformatics \| drug development \| hts \| knime \| pains \| rdkit	View Download (v1)
KNIME Original Uploader sauberns	RDKit-bioisosteres (v1) Created: 18/01/12 @ 03:42:13 \| Last updated: 18/01/12 @ 22:42:28 Credits: sauberns Attributions: RDKit-pains License: Creative Commons Attribution 3.0 Unported License 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: 9 times \| Downloaded: 1 time Tags (5): cheminformatics \| chemoinformatics \| drug development \| knime \| rdkit	View Download (v1)

Packs (2)

Creator:

Katy Wolstencroft

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

21 items in this pack

Comments: 0 | Viewed: 146 times | Downloaded: 23 times

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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...

3 items in this pack

Comments: 0 | Viewed: 32 times | Downloaded: 15 times

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