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Tag: cheminformatics

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

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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.

Created: 2009-10-15

Credits: User Egon Willighagen

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

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

Created: 2009-08-21

Credits: User Egon Willighagen

Workflow Create Ugi Library 001 (1)

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?

Created: 2008-12-04

Credits: User Jean-Claude Bradley

Creator

Pack KNIME workflows and associated data from Koch et. al...


Created: 2017-06-29 17:26:00 | Last updated: 2017-12-19 10:19:21

The pack provides the KNIME workflows and associated data from:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9Please browse the linked packs below.

4 items in this pack

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Workflow Indigo-pains-recursive (2)

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*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.Using the WEHI-10k reference set (embedded in ...

Created: 2013-08-13 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow Indigo-pains Workflow RDKit-pains-parallel

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

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

Created: 2009-10-23

Credits: User Egon Willighagen

Creator

Pack Pack #4 - Metabolome completion and metabolomics


Created: 2017-06-30 16:36:44 | Last updated: 2017-12-19 10:22:42

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-metabolomics workflow as well as (ii) all the associated data for the metabolome completion use case (see the main text for details, section 2.4 Metabolome completion and metabolo...

2 items in this pack

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Pack Pack #3 - Search for molecules maximizing biological...


Created: 2017-06-30 16:33:44 | Last updated: 2017-12-19 10:22:03

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-iQSAR workflow for the search of molecules of interest, (ii) the QSAR-model-aminoglycosides workflow that build a QSAR model for predicting the antibacterial activity, and (iii) t...

3 items in this pack

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Pack Pack #2 - Isomer enumeration (isomer transformation ...


Created: 2017-06-30 16:31:31 | Last updated: 2017-12-19 10:21:41

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-isomer-transformation worklfow, (ii) data for the enumeration of alkane isomers using the isomer transformation algorithm (see the main text for details, section 2.1 Isomer enumer...

5 items in this pack

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Pack Pack #1 - Isomer enumeration (canonical augmentation...


Created: 2017-06-30 16:29:21 | Last updated: 2017-12-19 10:20:58

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains the (i) RetroPath2.0-Mods-isomer-augmentation worklfow as well as (ii) the associated data for the enumeration of isomers using the canonical augmentation algorithm (see the main text for details, section ...

2 items in this pack

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