ZINC15:examples - Revision history

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	* [[ZINC15:videos]]		* [[ZINC15:videos]]
	* [[ZINC15:examples:screening]]		* [[ZINC15:examples:screening]]

			query ZINC using api
			time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?
			purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" \| tee 18.txt \| cat -n


	= Private access =		= Private access =

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	* [[ZINC15:videos]]		* [[ZINC15:videos]]
	* [[ZINC15:examples:screening]]		* [[ZINC15:examples:screening]]
	* [[ZINC15:examples:resources]]

	= Private access =		= Private access =

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	{{TOCright}}		{{TOCright}}
			= Introduction =
	Here are examples of what you can do with ZINC15, organized by		Here are examples of what you can do with ZINC15, organized by
	* a) whether our solution is web accessible (public) or requires ssh access (private)		* a) whether our solution is web accessible (public) or requires ssh access (private)
	and		and
	* level of difficulty - see [[ZINC15:Levels]] for difficulty levels.		* b) level of difficulty - see [[ZINC15:Levels]] for difficulty levels.
	~~Please see also [[ZINC15:videos]] for discussions of various topics and [[ZINC15:examples:screening]] and [[ZINC15:examples:resources]] for more examples~~.

	= Public Access =		= Public Access =
	[[ZINC15:examples:public]]		* [[ZINC15:examples:public]]
			* [[ZINC15:videos]]
			* [[ZINC15:examples:screening]]
			* [[ZINC15:examples:resources]]

			= Private access =
	= Private access~~. requires~~ ssh access or a private ZINC ~~copy =~~		These require ssh access or a private copy of ZINC
	[[ZINC15:examples:private]]		* [[ZINC15:examples:private]]

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

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 = Private access. requires ssh access or a private ZINC copy =
+[[ZINC15:examples:private]]
 = Examples mentioned in or implied by the 2015 paper =

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← Older revision		Revision as of 23:36, 1 October 2015
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	http://zinc15.docking.org/activities.txt:substance.zinc_id+substance.best_purchasability+substance.best_catalog+target.name+affinitynm?activity.affinitynm-gt=9		http://zinc15.docking.org/activities.txt:substance.zinc_id+substance.best_purchasability+substance.best_catalog+target.name+affinitynm?activity.affinitynm-gt=9

	[[Category:ZINC15]] [[Category:Idioms]]		Search by inchikey prefix

			translator:
			http://zinc15.docking.org/apps/mol/convert?from=c1ccccc1&to=inchikey

			blah
			http://zinc15.docking.org/substances?references-any-pubmed_id=14695814


			http://zinc15.docking.org/substances/?inchikey-startswith=LFQSCWFLJHTTHZ

			Search by inchikey
			http://zinc15.docking.org/substances/?inchikey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N

			Endogenous and Drug metabolites (ZINC, a new method to find problems in other databases)
			http://zinc15.docking.org/catalogs/hmdbendo/substances/?catalogs-any-short_name=hmdbdrug

			FDA approved but not in drugstore, generally this is due to stereochemistry issues in drugbank.
			http://zinc15.docking.org/catalogs/dbfda/substances/?~catalogs-any-short_name=drugstore


			first one: http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb

			second one: (correct): http://zinc15.docking.org/catalogs/lipid/substances/?catalogs-any-short_name=lipid

			blah
			http://zinc15.docking.org/catalogs/foodb/substances/subsets/endogenous

			Question: what compounds are in the "lipidomics" catalog but are NOT
			in HMDB (as we currently have it loaded):
			http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb

			thus, compounds sold by sigma aldrich that hit DRD2 and not HRH1 pace ChEMBL,10uM.
			http://zinc15.docking.org/catalogs/sial/substances/?genes-any-name=DRD2&~genes-any-name=HRH1

			Only one catalog, and it is sial:
			http://zinc15.docking.org/catalogs/sial/substances/?~catalogs-any-short_name-ne=sial
			We would like a variant for no other catalog of type 50,40,20,10 only. That's a request.

			Metabolites that look like ethanol:
			http://zinc15.docking.org/substances/subsets/metabolites/?ecfp4_fp-tanimoto-50=CCO
			(produced in the gut by the bacterial flora)

			Get fingerprint
			http://zinc15.docking.org/substances/ZINC000018011573.txt:ecfp4_fp.as_base64

			How many molecules are in pubchem?
			http://zinc15.docking.org/catalogs/pubchem/substances?special=count

			blah
			http://zinc15.docking.org/catalogs/pubchem/substances?special=count-wait

			blah
			http://zinc15.docking.org/majorclasses/?substances-any-purchasability=for-sale
			blah
			http://zinc15.docking.org/majorclasses/?substances-any-purchasability=not-for-sale
			blah
			http://zinc15.docking.org/majorclasses/?substances-memberof=biogenic

			[[Category:Tutorials]]
			[[Category:ZINC15]]
			[[Category:Idioms]]

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			Get supplier_codes for chembl20 compounds that match PAINS
			wget -O- 'http://zinc15.docking.org/catalogs/chembl20/substances.json:zinc_id+catalog_items+patterns?patterns-any-origin_name=pains&count=all' \| jq -r '[.zinc_id, (.patterns[] \| select(.origin_name == "pains") \| .name), (.catalog_items[] \| select(.catalog_short_name == "chembl20") \| .supplier_code)] \| @csv' \| csv --to-tsv \| tee chembl-patterns.txt

	[[Category:ZINC15]]		= substance-oriented =

			= gene-oriented =
			Compounds that are similar to dopamine and are endogenous human metabolites
			http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc(c(cc1CC[NH2])O)O
			OR
			http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=33882

			Similar to (drug) and has been in man
			http://zinc15.docking.org/substances/subsets/in-man.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc2c(cc1O)C[C@H](CC2)N

			http://zinc15.docking.org/genes

			list of genes and their major classes
			http://zinc15.docking.org/genes/txt:name%2Cdescription%2Ctarget_class.name%2Ctarget_class.major_target_class.name/

			list of target classes
			http://zinc15.docking.org/targetclasses.txt:name

			list of major target classes
			http://zinc15.docking.org/majorclasses.txt:name

			enzyme genes
			http://zinc15.docking.org/genes.txt:name%2Cdescription+target_class.name?majorclass.name=enzyme

			http://zinc15.docking.org/targets.txt:gene.name+majorclass.name%20eq%20enzyme

			what it does
			.../substance.structure similarto c1ccccc1CCCOC within .7 using tanimoto

			blah
			/substance/txt:zinc_id/substance isa metabolite

			asdfasdf
			/substances/txt:zinc_id?sort=substance.structure+near+c1ccccc1CCNC+using+dice

			The organism table (modified from ChEMBL)
			http://zinc15.docking.org/organisms/txt:organism_id,code,description/

			Table of Dopamine receptor genes
			http://zinc15.docking.org/targets.txt:name,description,gene.description,uniprot,chembl,gene_fk,gene.name?gene.name-startswith=DRD

			List of chemotype clusters (not too useful, but proof of concept)
			http://zinc15.docking.org/clusters.txt:number+gene.name

			All compound-target pairs with activity of 1nM or better
			http://zinc15.docking.org/activities.txt:substance.zinc_id+substance.best_purchasability+substance.best_catalog+target.name+affinitynm?activity.affinitynm-gt=9

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

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	Which compounds are in Drugbank but not in ChEMBL Drugstore?		Which compounds are in Drugbank but not in ChEMBL Drugstore?
	write me here ???		write me here ???

			Which FDA approved drugs are associated with publications describing direct binding ligand affinity data:
			http://zinc15.docking.org/substances/subsets/fda/having/references/

	Which genes have a ligand reported that binds at 10nM concentration or better?		Which genes have a ligand reported that binds at 10nM concentration or better?

Frodo: /* Private access required - ssh access or a private ZINC installation required */ asdf

2015-10-01T19:58:45Z

Private access required - ssh access or a private ZINC installation required: asdf

← Older revision		Revision as of 19:58, 1 October 2015
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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.

	= Private access ~~required -~~ ssh access or a private ZINC ~~installation required~~ =		= Private access. requires ssh access or a private ZINC copy =

	== Level 4 - privileged access ==		== Level 4 - privileged access ==