ZINC15 patterns - Revision history

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2017-02-20T17:26:34Z

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	http://zinc15.docking.org/substances/?substance.patterns-any-type_name=weak-electrophile		http://zinc15.docking.org/substances/?substance.patterns-any-type_name=weak-electrophile

			== pains and aggregators ==

			curl http://zinc15.docking.org/patterns/apps/checker/ -F upload=@fda.smi -F pains=y -F aggregators=y -F output_format=txt \| tee results


	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-07-14T01:31:43Z

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	Molecules with this pattern:		Molecules with this pattern:
	http://zinc15.docking.org/substances/?pattern.name=quinone_a_370_		http://zinc15.docking.org/substances/?pattern.name=quinone_a_370_

			http://zinc15.docking.org/substances/?substance.patterns-any-type_name=weak-electrophile

	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-07-14T00:50:00Z

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	Drugs with any smarts pattern:		Drugs with any smarts pattern:
	http://zinc15.docking.org/substances/subsets/fda?pattern.origin_fk=2		http://zinc15.docking.org/substances/subsets/fda?pattern.origin_fk=2

			Molecules with this pattern:
			http://zinc15.docking.org/substances/?pattern.name=quinone_a_370_

	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-07-14T00:45:37Z

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	http://zinc15.docking.org/patterns/?description-startswith=imidazole		http://zinc15.docking.org/patterns/?description-startswith=imidazole

			http://zinc15.docking.org/patterns/?description-contains=370

			http://zinc15.docking.org/patterns/?description-contains=quinone

			Drugs with a quinone pattern
			http://zinc15.docking.org/substances/subsets/fda?pattern.description-contains=quinone

			Drugs with any smarts pattern:
			http://zinc15.docking.org/substances/subsets/fda?pattern.origin_fk=2

	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-07-14T00:38:43Z

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	4 - permissive - allows 12, 13, 14, 15, 16 but not 3 and 4, the chemistry that is too hot for buffer conditions.		4 - permissive - allows 12, 13, 14, 15, 16 but not 3 and 4, the chemistry that is too hot for buffer conditions.
	5 - hot. 3D models of these molecule do not get built for docking (boronic acids, Sn-containing, Si-containing, because we don't have parameters)		5 - hot. 3D models of these molecule do not get built for docking (boronic acids, Sn-containing, Si-containing, because we don't have parameters)


			http://zinc15.docking.org/patterns/?description-startswith=imidazole

	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-06-21T19:38:34Z

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← Older revision		Revision as of 19:38, 21 June 2015
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	* 13. too greasy / insoluble		* 13. too greasy / insoluble

			== subpat ==
			* links individual molecules to individual patterns


			Then we go on to calculate a "cleanness ranking" for each ZINC ID using the above as follows:
	Then we go on to calculate a "cleanness ranking" using the above as follows:

	0 - clean - molecule has none of these pattern, so may be boring too		0 - clean - molecule has none of these pattern, so may be boring too
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	3 - standard - additionally allows 1,2, 5, 10, 11		3 - standard - additionally allows 1,2, 5, 10, 11
	4 - permissive - allows 12, 13, 14, 15, 16 but not 3 and 4, the chemistry that is too hot for buffer conditions.		4 - permissive - allows 12, 13, 14, 15, 16 but not 3 and 4, the chemistry that is too hot for buffer conditions.
	5 - hot, ~~but~~ we don't ~~allow this.~~		5 - hot. 3D models of these molecule do not get built for docking (boronic acids, Sn-containing, Si-containing, because we don't have parameters)

	[[Category:ZINC15]]		[[Category:ZINC15]]

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2015-06-21T19:36:52Z

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New page

We compute which molecules have which patterns. We use these for
* the "clean" feature
* identifying covalent warheads
* preventing some molecules from being built for 3D non-covalent docking (e.g. Si, B, Sn containing)

The tables are as follows:
== pattern ==
This table holds the smarts patterns, a fk to the origin of the pattern, an english description, a fk to the type of pattern it is, and the max sub_id that has been processed (i.e. how up to date it is)

== pattern_origin ==
So far, we are keeping track of 4 pattern origins:
* traditional "clean" filters we've used for 10 years to build ZINC.
* PAINS (including a good number we disagree with, but we don't have the patience to argue about)
* New filters that we noticed were missing in ZINC12
* covalent warhead (functional group). / could also be a non-covalent warhead, like a hydroxamate. Watch out for protecting groups! complicated!

== pattern_type ==
These give you some idea of what we think the pattern is for. Frankly, it is kinda arbitrary. It is a bit of documentation for the future.
* 1. weak electrophile (reasonable chance it won't react in an assay) (e.g. C=O, michael acceptor)
* 2. weak nucleophile ( e.g. SH )
* 14. moderate electrophiles (e.g. epoxide, alkyl halides)
* 15. moderate nucleophiles (could be tolerated in an assay or drug) e.g. alkyl halide.
* 16. moderately reactive (and not 14 or 15). (e.g. peroxide)
* 3. strong electrophile, incompatible with buffer conditions (e.g. boronic acid.)
* 4. strong nucleophile (e.g. ...)
* 5. Chromophore. (e.g. ...)
* 6. known aggregator
* 7. aggregator analog
* 8. we doubt, but pains says so
* 9. unclear, but we accept
* 10 unstable in buffer (e.g. S-S bond)
* 11. not cell penetrant (e.g. quarts)
* 12. too floppy for docking (entropy)
* 13. too greasy / insoluble

Then we go on to calculate a "cleanness ranking" using the above as follows:

0 - clean - molecule has none of these pattern, so may be boring too
1 - pains-free - molecule hits no pains (0 and 1 may be the same thing, not sure)
2 - bksclean - allows 6,7,8,9
3 - standard - additionally allows 1,2, 5, 10, 11
4 - permissive - allows 12, 13, 14, 15, 16 but not 3 and 4, the chemistry that is too hot for buffer conditions.
5 - hot, but we don't allow this.

[[Category:ZINC15]]