ZINC15:examples:public - Revision history

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2019-10-29T21:41:42Z

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	How many ChEMBL targets have at least one purchasable compound for sale?		How many ChEMBL targets have at least one purchasable compound for sale?
	http://zinc15.docking.org/~~targets~~/having/substances/subsets/for-sale/		http://zinc15.docking.org/genes/having/substances/subsets/for-sale/
			or
			http://zinc15.docking.org/orthologs/having/substances/subsets/for-sale/

	How many ligands for ligand gated ion channels are for sale?		How many ligands for ligand gated ion channels are for sale?

TBalius at 20:21, 18 November 2016

2016-11-18T20:21:41Z

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	Download a table of data with smiles, zinc_id, mwt, logP, and rotatable bonds.		Download a table of data with smiles, zinc_id, mwt, logP, and rotatable bonds.
	http://zinc15.docking.org/substances.txt:smiles,zinc_id,mwt,logp~~,rot_bond~~		http://zinc15.docking.org/substances.txt:smiles+zinc_id+mwt+logp+rb

	To get compounds that bind DRD2		To get compounds that bind DRD2

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 Purch:
   select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and g.organism_fk = 2 and c.purchasable > 9
 Back to [[ZINC15:examples]]

Frodo: /* Figure 2 */ asdf

2015-10-07T18:11:35Z

Figure 2: asdf

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	Non-purch final:		Non-purch final:
	~~psql -h samekh -U test zinc15 -c "~~select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 1 group by g.name ~~" > 1-10um.txt~~		select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 1 group by g.name

	Purch final:		Purch final:
	~~psql -h samekh -U test zinc15 -c "~~select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 2 and c.purchasable > 9 group by g.name~~" > 2-10um-purch.txt~~		select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 2 and c.purchasable > 9 group by g.name

	~~Unknown~~
	~~http://api.docking.org/v1/activities/txt:target.gene.name,sub_id_fk,affinitynm,substance.best_purchasbility~~

	New non-purch		New non-purch
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	Purch:		Purch:
	select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and g.organism_fk = 2 and c.purchasable > 9 ~~group by g.name limit 10;~~		select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and g.organism_fk = 2 and c.purchasable > 9

	Back to [[ZINC15:examples]]		Back to [[ZINC15:examples]]

Frodo: /* Examples mentioned in or implied by the 2015 paper */ sdf

2015-10-07T18:10:23Z

Examples mentioned in or implied by the 2015 paper: sdf

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	Using a bit of python can dramatically extend the power of the ZINC website.		Using a bit of python can dramatically extend the power of the ZINC website.

	~~= Examples mentioned in or implied by the 2015 paper =~~

	== NEW TABLE 8 ==		== NEW TABLE 8 ==

Frodo: /* Level 2 questions - edit URL by hand */ asdf

2015-10-07T18:09:58Z

Level 2 questions - edit URL by hand: asdf

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	== Level 2 questions - edit URL by hand ==		== Level 2 questions - edit URL by hand ==
	This is usually because we have not yet gotten around to writing a graphical interface for this class of questions.		This is usually because we have not yet gotten around to writing a graphical interface for this class of questions.

			At the moment (Oct 7, 2015) many constraints (after the ?) still need to be edited by hand.
			Another thing is the having clause, currently by hand, but soon, graphically.


	Description		Description

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Show changes

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2015-10-01T23:50:02Z

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	{{TOCright}}		{{TOCright}}
			Examples organized by [[ZINC15:Levels]], part of [[ZINC15:examples]].
	== Level 1 questions - one-liners, using webpage ==		== Level 1 questions - one-liners, using webpage ==
	Ligands for Dopamine D2 receptor, and those you can buy on the second line, and those you can get in 2 weeks on the third		Ligands for Dopamine D2 receptor, and those you can buy on the second line, and those you can get in 2 weeks on the third

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2015-10-01T23:48:43Z

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			{{TOCright}}
	== Level 1 questions - one-liners, using webpage ==		== Level 1 questions - one-liners, using webpage ==
	Ligands for Dopamine D2 receptor, and those you can buy on the second line, and those you can get in 2 weeks on the third		Ligands for Dopamine D2 receptor, and those you can buy on the second line, and those you can get in 2 weeks on the third

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			We illustrate the use of the [[ZINC15]] interface with examples for each [[resource]] type, ordered by increasing complexity.

			== Substances ==
			Browse all substances in ZINC,
			http://zinc15.docking.org/substances
			Browse available substance subsets
			http://zinc15.docking.org/substances/subsets
			To ask for purchasable metabolites
			http://zinc15.docking.org/substances/subsets/purchasable+metabolites
			Substance "home page", where you can search for molecules
			http://zinc15.docking.org/substances/home
			Substance help page
			http://zinc15.docking.org/substances/help
			Download substance in SMILES format (likewise for .sdf, .mol2, .json, .xml, .txt, .xls, .csv and .tsv formats.)
			http://zinc15.docking.org/substances.smi
			Download a table of data with smiles, zinc_id, mwt, logP, and rotatable bonds.
			http://zinc15.docking.org/substances.txt:smiles,zinc_id,mwt,logp,rot_bond
			To get a list of all possible columns:
			???????
			To get compounds that bind DRD2
			http://zinc15.docking.org/substances?genes-any-name=DRD2
			To get compounds similar to Aspirin
			http://zinc15.docking.org/substances?ecfp4_fp=53 (the ZINC ID for Aspirin)
			To get compounds containing a primary basic amine
			http://zinc15.docking.org/substances?structure-contains=[CX4][ND1]
			To get compounds similar to 2-chlorophenol
			http://zinc15.docking.org/substances/ecfp4_fp-tanimoto=Clc1ccccc1O
			To get compounds reported to bind DRD2 and not HRH1 and are purchasable and are FDA approved drugs, and contain a primary amine:
			http://zinc15.docking.org/subtances/subsets/purchsable+fda?genes-any-name=DRD2&~genes-any-name=HRH1&structure-contains=[CX4][ND1]

			We now take up the other resources in ZINC in turn.

			== Catalogs ==
			To list all catalogs
			http://zinc15.docking.org/catalogs

			Catalog detail for Sigma Aldrich
			http://zinc15.docking.org/catalogs/sial

			To list the catalog items that Enamine sells:
			http://zinc15.docking.org/catalogs/enamine/items

			To get all FDA approved drugs
			http://zinc15.docking.org/catalogs/dbfda/substances

			To get purchasable building blocks containing a nitrile (note # is not valid in URLs %23 is urlencoded #).
			http://zinc15.docking.org/catalogs/subsets/purchasable+bb?structure-contains=C%23N

			== Genes ==
			To get a list of all genes
			http://zinc15.docking.org/genes
			All gene subsets
			http://zinc15.docking.org/genes/subsets
			All compounds that hit SLC6A3
			http://zinc15.docking.org/genes/SLC6A3/substances

			http://zinc15.docking.org/genes/KITH/catalogs

			http://zinc15.docking.org/genes/HTR2A/items

			http://zinc15.docking.org/genes/SLC6A3/predictions

			== Predictions ==

			predictions

			== Target Classes ==

			targetclasses

			== Catalog Items ==

			catitems

			== Protomers (ready-to-dock 3D representations) ==
			protomers

	Back to [[ZINC15:examples]]		Back to [[ZINC15:examples]]