RDKit-pains-parallel

Created: 2011-10-13 02:33:12      Last updated: 2015-12-01 00:56:44

 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 set from WEHI[1] which is used by default as input if no other file is chosen.

The RDKit nodes require installation of the 'community nodes' in KNIME. See http://tech.knime.org/community-installation

Based on simple sub-structure workflow by James Davidson
http://tech.knime.org/forum/rdkit/substructure-search-with-rdkit
Modified to use SD/SMILES file as input, or manual SMILES entry, or database search.

1. J. B. Baell and G. A. Holloway, Journal of Medicinal Chemistry, 2010, 53, 2719-2749, http://dx.doi.org/10.1021/jm901137j

2. Rajarshi Guha. "PAINS Substructure Filters as SMARTS. 2010-11-14."
http://blog.rguha.net/?p=850. Accessed: 2010-11-14. (Archived by
WebCite® at http://www.webcitation.org/5uF4wHEpB)

Information Preview

Medium

Information Run

Not available


Information Workflow Components

Not available

Information Workflow Type

KNIME

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

View version:

Information Credits (1)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

Information Tags (7)

Log in to add Tags

Information Shared with Groups (1)

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (1)

(Workflows/Files)

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (1)

Log in to make a comment

  • Thursday 19 November 2015 05:03:11 (UTC)

    Now using KNIME 3 and RDKit version of PAINS queries.




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.