More cool zinc15 tricks - Revision history

Enkhjargal at 00:11, 1 February 2017

2017-02-01T00:11:24Z

← Older revision		Revision as of 00:11, 1 February 2017
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	Upload a set of molecules, look them up in ZINC, output them if a) it is in ZINC, b) it matches the pattern		Upload a set of molecules, look them up in ZINC, output them if a) it is in ZINC, b) it matches the pattern
	curl -X POST -u user:pass -H "Content-Type: multipart/form-data" -F upload=@test2.smi -F identifiers=true -F structures=true -F charges=true -F scaffolds=true -F multiple=true \		curl http://zinc15.docking.org/substances/resolved/ -F upload=@test_substances.txt.save -F identifiers=true -F structures=true -F multiple=true -F names=true -F output_format=smi > test.smi
	"http://band.desktop.ucsf.bkslab.org:8088/substances/resolved/" -F output_format=smi -F output_fields=smiles,zinc_id -F 'structure-contains=n1ccccc1' -F suppliers=		(curl -X POST -u user:pass -H "Content-Type: multipart/form-data" -F upload=@test2.smi -F identifiers=true -F structures=true -F charges=true -F scaffolds=true -F multiple=true \
			"http://band.desktop.ucsf.bkslab.org:8088/substances/resolved/" -F output_format=smi -F output_fields=smiles,zinc_id -F 'structure-contains=n1ccccc1' -F suppliers=)

	Then, look up the targets of these compound:		Then, look up the targets of these compound:

Frodo: asdf

2015-07-11T05:20:42Z

asdf

← Older revision		Revision as of 05:20, 11 July 2015
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	Then, look up the targets of these compound:		Then, look up the targets of these compound:
	wget --user xxx--password xxx -o log -O final.txt "http://zinc15.docking.org/activities.txt" -F zinc_id-in=@abc.txt -F count=all		wget --user xxx--password xxx -o log -O final.txt "http://zinc15.docking.org/activities.txt" -F zinc_id-in=@abc.txt -F count=all

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

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

Frodo: asdf

2015-07-09T22:00:59Z

asdf

← Older revision		Revision as of 22:00, 9 July 2015
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	Then, look up the targets of these compound:		Then, look up the targets of these compound:
	wget --user ~~gpcr~~ --password ~~xtal~~ -o log -O final.txt "http://zinc15.docking.org/activities.txt" -F zinc_id-in=@abc.txt -F count=all		wget --user xxx--password xxx -o log -O final.txt "http://zinc15.docking.org/activities.txt" -F zinc_id-in=@abc.txt -F count=all

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

Frodo: qwer

2015-07-09T22:00:18Z

qwer

← Older revision		Revision as of 22:00, 9 July 2015
Line 25:		Line 25:
	curl -X POST -u user:pass -H "Content-Type: multipart/form-data" -F upload=@test2.smi -F identifiers=true -F structures=true -F charges=true -F scaffolds=true -F multiple=true \		curl -X POST -u user:pass -H "Content-Type: multipart/form-data" -F upload=@test2.smi -F identifiers=true -F structures=true -F charges=true -F scaffolds=true -F multiple=true \
	"http://band.desktop.ucsf.bkslab.org:8088/substances/resolved/" -F output_format=smi -F output_fields=smiles,zinc_id -F 'structure-contains=n1ccccc1' -F suppliers=		"http://band.desktop.ucsf.bkslab.org:8088/substances/resolved/" -F output_format=smi -F output_fields=smiles,zinc_id -F 'structure-contains=n1ccccc1' -F suppliers=

			Then, look up the targets of these compound:
			wget --user gpcr --password xtal -o log -O final.txt "http://zinc15.docking.org/activities.txt" -F zinc_id-in=@abc.txt -F count=all

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

Frodo: asdf

2015-07-08T20:13:12Z

asdf

← Older revision		Revision as of 20:13, 8 July 2015
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	http://zinc15.docking.org/genes/SLC5A1/substances?ecfp4_fp-dice=ZINC000003875408		http://zinc15.docking.org/genes/SLC5A1/substances?ecfp4_fp-dice=ZINC000003875408

			Purchasable compounds for SLC5A1, ordered by decreasing similarity to ZINC000003875408
			http://zinc15.docking.org/genes/SLC5A1/substances/subsets/purchasable+in-vitro/?ecfp4_fp-dice=ZINC000003875408

	http://~~zinc15~~.~~docking~~.org~~/genes/SLC5A1~~/substances/~~subsets~~/~~purchasable+in~~-~~vitro/?ecfp4_fp~~-~~dice~~=~~ZINC000003875408~~		Upload a set of molecules, look them up in ZINC, output them if a) it is in ZINC, b) it matches the pattern
			curl -X POST -u user:pass -H "Content-Type: multipart/form-data" -F upload=@test2.smi -F identifiers=true -F structures=true -F charges=true -F scaffolds=true -F multiple=true \
			"http://band.desktop.ucsf.bkslab.org:8088/substances/resolved/" -F output_format=smi -F output_fields=smiles,zinc_id -F 'structure-contains=n1ccccc1' -F suppliers=

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

Frodo: asdf

2015-07-08T19:21:03Z

asdf

← Older revision		Revision as of 19:21, 8 July 2015
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	http://zinc15.docking.org:8015/activities.txt:substance.smiles,substance.sub_id,substance.purchasability?subclass.name:eq=GPCR-F&substance.purchasability:gt=9&count=all		http://zinc15.docking.org:8015/activities.txt:substance.smiles,substance.sub_id,substance.purchasability?subclass.name:eq=GPCR-F&substance.purchasability:gt=9&count=all

			SLC5A1 glucose cotransporter and in chembl20
			http://zinc15.docking.org/genes/SLC5A1/substances/?catalog.short_name=chembl20

			Analogs of ZINC000003875408 that bind to SLC5A1:
			http://zinc15.docking.org/genes/SLC5A1/substances?ecfp4_fp-dice=ZINC000003875408


			http://zinc15.docking.org/genes/SLC5A1/substances/subsets/purchasable+in-vitro/?ecfp4_fp-dice=ZINC000003875408

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

Frodo: asdf

2015-07-08T17:02:39Z

asdf

← Older revision		Revision as of 17:02, 8 July 2015
Line 6:		Line 6:
	A second way of asking the same question:		A second way of asking the same question:
	http://zinc15.docking.org/substances.smi:zinc_id,purchasability?features-contains=203&~features-contains=202&count=all		http://zinc15.docking.org/substances.smi:zinc_id,purchasability?features-contains=203&~features-contains=202&count=all

			primary amines, building blocks, for sale
			http://zinc15.docking.org:8015/substances.txt:smiles,sub_id,purchasability?substance.structure:contains=[ND1][CX4]&catalog.bb=True&substance.purchasability:gt=9&count=all

			purchasable class-F gpcr ligands:
			http://zinc15.docking.org:8015/activities.txt:substance.smiles,substance.sub_id,substance.purchasability?subclass.name:eq=GPCR-F&substance.purchasability:gt=9&count=all


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

Frodo: asdf

2015-07-08T16:56:17Z

asdf

New page

Here are questions you can ask. Ideally, work these into a tutorial of some kind:

Natural products = biogenic minus metabolites:
http://zinc15.docking.org/substances/subsets/biogenic.smi:zinc_id,purchasability?~features-contains=202&count=all

A second way of asking the same question:
http://zinc15.docking.org/substances.smi:zinc_id,purchasability?features-contains=203&~features-contains=202&count=all

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