RDKit-pains

Created: 2011-02-07 02:05:36 Last updated: 2015-11-19 04:55:51

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Implementation of the PAINS filters[1] using the RDKit (1.0.0.0000763) nodes in KNIME (2.3.1). Original PAINS filters published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with 10k reference structure set from WEHI[1] which is used by default as input if no other file 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)

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sauberns

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RDKit-pains

Created by sauberns on Monday 07 February 2011 02:05:35 (UTC)

Last edited by sauberns on Monday 07 February 2011 02:22:15 (UTC)
RDKit-pains

Created by sauberns on Thursday 10 March 2011 00:51:05 (UTC)

Last edited by sauberns on Thursday 05 May 2011 08:44:04 (UTC)

Revision comment:

Minor correction to function in jython node.
RDKit-pains

Created by sauberns on Tuesday 10 May 2011 06:23:33 (UTC)

Last edited by sauberns on Monday 08 August 2011 11:11:40 (UTC)

Revision comment:

Exporting from MacOS KNIME looses flow variable settings! This version is the same as ver 2, but exported from Linux KNIME.
RDKit-pains

Created by sauberns on Thursday 19 November 2015 04:53:35 (UTC)

Last edited by sauberns on Thursday 19 November 2015 04:55:51 (UTC)

Revision comment:

*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ***

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sauberns

RDKit 2.0.0.1088 now matches 636 structures, up from 329 reported in our paper, but matches 2 additional structures not matched by the SLN filters.

See discussion on RDKit list: http://goo.gl/NVIgy

sauberns

The updated PAINS filters from the RDKit developer are resulting in improved results:

http://rdkit.blogspot.com/2015/08/curating-pains-filters.html

Just waiting on the nodes to be updated in KNIME before updating the workflows here, but you can grab the filters from the above link if you can't wait.

sauberns	Thursday 19 November 2015 04:57:48 (UTC)
	RDKit nodes are now available in KNIME 3, so version 4 is now based on KNIME 3.0.1 and the updated PAINS filters from the RDKit repository.

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