ZINC:FAQ - Revision history

Frodo at 15:42, 11 March 2014

2014-03-11T15:42:13Z

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	Frequently asked questions about ZINC. [[FAQ \|Other FAQs]]		Frequently asked questions about ZINC. [[:Category:FAQ \|Other FAQs]]
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Frodo at 15:41, 11 March 2014

2014-03-11T15:41:35Z

← Older revision		Revision as of 15:41, 11 March 2014
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	Frequently asked questions about ZINC. ~~Other FAQs:~~ [[~~DOCK:FAQ]], [[DUD:FAQ]], [[DOCK Blaster:~~FAQ]]		Frequently asked questions about ZINC. [[FAQ \|Other FAQs]]
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Therese: 13 revisions

2012-10-08T20:33:18Z

13 revisions

← Older revision

Revision as of 20:33, 8 October 2012

Frodo at 01:59, 23 February 2012

2012-02-23T01:59:18Z

← Older revision		Revision as of 01:59, 23 February 2012
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	Frequently asked questions about ZINC.		Frequently asked questions about ZINC. Other FAQs: [[DOCK:FAQ]], [[DUD:FAQ]], [[DOCK Blaster:FAQ]]

	Other FAQs: [[DOCK:FAQ]], [[DUD:FAQ]], [[DOCK Blaster:FAQ]]
	{{TOCright}}		{{TOCright}}

Frodo at 01:01, 23 February 2012

2012-02-23T01:01:12Z

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	~~Here are frequently~~ asked questions about ZINC.		Frequently asked questions about ZINC.

			Other FAQs: [[DOCK:FAQ]], [[DUD:FAQ]], [[DOCK Blaster:FAQ]]
	{{TOCright}}		{{TOCright}}
	~~Note that other FAQs are also available.~~
	* [[DOCK:FAQ]]
	* [[DUD:FAQ]]
	* [[DOCK Blaster:FAQ]]
	* [[THC:FAQ]]
	* [[FAQ]] for everything not covered by one of those products.

			= What is the version (how to cite) ? =
			The interface is version 12, released in January 2012. The next version will be in January 2013, and a beta will appear in the fall.

			The subsets of ZINC are updated regularly. Each subset has a release date and the total number of molecules. We recommend you quote these to specify which version you used.

	~~== How do I get arbitrary subsets~~ of ~~ZINC? ==~~		Thus you might say: We used ZINC version 12 (Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82). We downloaded the standard lead-like subset of 4,554,059 molecules dated 2012-02-06 on February 20, 2012.

	~~Q1. I am trying to generate a subset of your~~ "~~drug-like~~" molecule ~~subset for~~		We recommend that you always download the "Purchasing Info" in addition to the actual molecule structure files every time you download ZINC. This provides you with static purchasing information, in case in the meantime the molecules goes off the market and becomes unavailable.
	~~virtual screening~~. ~~I was thinking your 60% diversity group (about 12~~,~~000~~
	molecules~~) would be a place to start, and I downloaded~~ the ~~.smi file. I~~
	~~relatively new to chemoinformatics~~ and ~~I was wondering if there is an~~
	~~elegant way to separate the compounds listed in the~~ .~~smi file from the~~
	~~larger library containing the mol2 files from the 2,000,000 "usual" set that~~
	~~I have downloaded from ZINC?~~

	~~A1.~~		= What is the purpose of ZINC? =
	~~wget http://zinc8.docking.org/subset1/3/3_t60.smi~~		The purpose of ZINC is to simplify ligand discovery for biology. A primary aim is screening library for molecular docking, and also for chemical informatics. ZINC aims to be current with correct purchasing information, to enable research.
	~~awk '{print $2}' 3_t60.smi >! codes~~
	~~sed -e 's/^/fget2.pl~~?~~f=m\&l=0\&z~~=~~/' codes > codes2~~
	~~wget -O all~~.~~mol2 -a listing~~ ~~-B http://zinc8.docking~~.~~org/ -i codes2~~

			= What can I do with ZINC? =
			You can use ZINC to make your life easier. You can use it for docking, for cheminformatics, for looking up molecules, for finding analogs by similarity, and for simply exploring vendors and the compounds they sell.

	~~l indicates the pH model. 0~~=~~reference (pH 7), 1~~=~~mid (5~~.~~75-8.25)~~, ~~2=hi (7-8~~.~~5), 3=lo (4~~.~~5-6)~~		= What sort of people is ZINC designed for? =
			ZINC is aimed at professional researchers seeking new molecules to test in biological experiments. It is used by graduate students, postdoctoral fellows and established researchers in pharmaceutical companies, in universities, in government research labs, and in biotechs and startup companies. ZINC is free to use for everyone.

			= How do I download ZINC? on Windows? =
			Every subset page and every vendor page has a special link for downloading the subset on Windows and on Unix, which includes Macs. We have a You Tube video which explains how to do this: http://youtube.com/user/chemistry4biology

	== I want ~~a hierarchy format database based~~ on ~~ZINC IDs~~. ==		= Do I want usual or single or something else? =
			If your docking program calculates protonation states and tautomers on the fly, then you want single. If you are doing cheminformatics, you probably want your SMILES as single. If you are doing molecular docking, you probably want usual, which includes relevant molecular forms between pH 6 and 8. If you are docking to metalloenzymes you want the metal subsets, which includes additional high pH forms.

	~~A2.~~		= Do I want lead-like or fragment-like or drug-like or something else? =
	~~create file "hits.txt" containing one ZINC ID per row.~~		If the binding site is very small, or if you are using a biophysical assay such as NMR or SPR, then you may want fragment-like. In most other cases, lead-like is the best choice for discovery projects.
	~~sed -e 's/^/fget2.pl?f=h\&l=0\&z~~=~~/' hits.txt > ref.txt~~
	~~wget~~ -~~O ref.db~~ -~~a listing~~ -~~B http://zinc.docking.org/ -i ref.txt~~
	~~The previous line gets~~ the ~~"reference" (pH 7) models. For additional "usual" forms~~, ~~use l=1.~~
	~~sed -e 's/^/fget2.pl?f=h\&l=1\&z=/' hits.txt > mid.txt~~
	~~wget -O mid.db -~~a ~~listing -B http://zinc.docking.org/~~ -~~i mid.txt~~
	~~Note we recommend splitting hits~~.~~txt into sets of 1000 ZINC IDs each~~, ~~thus:~~
	~~split~~ -~~l hits~~.~~txt~~
	~~foreach i (x??)~~
	~~sed ...~~
	~~wget ...~~
	~~end~~
	~~Please let us know if this is not clear!~~

			= Do I want standard, clean or now subsets? =
			Clean: If you can tollerate a high false positive rate and you want more chemistry, you probably want a standard subset. If you are new to screening or unsure about what you are doing, a clean subset may be a better choice. Clean subsets provide a filtered subset of chemical space that is less prone to artifactual hits, at a small cost of sacrificing chemistry.

	~~== Is there a script that does all of this? ==~~		Now: If you cannot wait 6-10 weeks for your compounds to arrive, you should choose the Now subsets. If you can afford to wait that long, you are better off not using Now, because you can access far more chemistry with the standard subsets.
	A3. ~~Yes~~, ~~Peter Kolb wrote one (thanks Peter). Download it here....~~
	~~[http://zinc.docking.org/scripts/get.db.from.id.sh]~~.

			= Can I script ZINC? =
			Yes. You can write URLs that deliver formatted results. See the [[ZINC:Command language]]. See also the [[Quick Search Bar]].

	~~Here is how to use this script.~~		= How are partial charges computed in ZINC? =

	~~First, put the ZINC IDs you want to get into a file, say "list1"~~

	~~Second, put the list of lists into a file, call this "masterlist"~~
	~~(i.e. line 1 of masterlist is contains 5 characters: list1~~

	~~Invoke the program~~

	~~chmod a+rx get.db.from.id.sh (as downloaded above)~~
	~~./get.db.from.id.sh masterlist 0 mol2 ; # to get "reference" molecules (0) in mol2 format~~
	~~./get.db.from.id.sh masterlist 1 mol2 ; # to get "additional physiological (mid, 1) in mol2~~

	~~Good luck!~~


	== How are partial charges computed in ZINC? ==

	The partial charges are computed by AMSOL 6 using the SM5.42R solvation model in organic solvent. The AMSOL input parameters look like the following:		The partial charges are computed by AMSOL 6 using the SM5.42R solvation model in organic solvent. The AMSOL input parameters look like the following:
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	(thanks to Michael Mysinger for this phrasing)		(thanks to Michael Mysinger for this phrasing)

			= I am a vendor: How can I get my catalog added to ZINC? =
			Please contact John Irwin who can help you do this.

	~~-- John Irwin~~, ~~Aug 2009~~		= Can I download everything? =
			Yes, there is an everything subset. It is here: [http://zinc.docking.org/subsets/everything http://zinc.docking.org/subsets/everything].

			= Can I use the old version? =
			Old versions of ZINC still exist, but they are not recommended, and have been partially disabled. If you feel you need to use an old version, we would like to hear from you why.

	[[Category:FAQ]]		[[Category:FAQ]]
	[[Category:ZINC]]		[[Category:ZINC]]

Frodo at 23:46, 28 June 2011

2011-06-28T23:46:11Z

← Older revision		Revision as of 23:46, 28 June 2011
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	Here are frequently asked questions about ZINC.		Here are frequently asked questions about ZINC.

			{{TOCright}}
			Note that other FAQs are also available.
	* [[DOCK:FAQ]]		* [[DOCK:FAQ]]
	* [[DUD:FAQ]]		* [[DUD:FAQ]]
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	* [[THC:FAQ]]		* [[THC:FAQ]]
	* [[FAQ]] for everything not covered by one of those products.		* [[FAQ]] for everything not covered by one of those products.



	== How do I get arbitrary subsets of ZINC? ==		== How do I get arbitrary subsets of ZINC? ==

Frodo at 16:05, 10 August 2009

2009-08-10T16:05:06Z

← Older revision		Revision as of 16:05, 10 August 2009
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	* [[THC:FAQ]]		* [[THC:FAQ]]
	* [[FAQ]] for everything not covered by one of those products.		* [[FAQ]] for everything not covered by one of those products.

			== How do I get arbitrary subsets of ZINC? ==

	Q1. I am trying to generate a subset of your "drug-like" molecule subset for		Q1. I am trying to generate a subset of your "drug-like" molecule subset for
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	~~Q2.~~ I want a hierarchy format database based on ZINC IDs.		== I want a hierarchy format database based on ZINC IDs. ==

	A2.		A2.
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	~~Q3.~~ Is there a script that does all of this?		== Is there a script that does all of this? ==

	A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....		A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....
	[http://zinc.docking.org/scripts/get.db.from.id.sh].		[http://zinc.docking.org/scripts/get.db.from.id.sh].
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	-- John Irwin, ~~March~~ 2009		== How are partial charges computed in ZINC? ==

			The partial charges are computed by AMSOL 6 using the SM5.42R solvation model in organic solvent. The AMSOL input parameters look like the following:

			CHARGE=$netchg AM1 1SCF CART TLIMIT=1 GEO-OK SM5.42R
			& SOLVNT=GENORG IOFR=1.4345 ALPHA=0.00 BETA=0.00 GAMMA=38.93
			& DIELEC=2.06 FACARB=0.00 FEHALO=0.00

			We only calculate the charges on one ligand conformation, but we use them for the whole ligand conformational ensemble.
			(thanks to Michael Mysinger for this phrasing)


			-- John Irwin, Aug 2009


	[[Category:FAQ]]		[[Category:FAQ]]
	[[Category:ZINC]]		[[Category:ZINC]]

Frodo at 01:07, 7 August 2009

2009-08-07T01:07:46Z

← Older revision		Revision as of 01:07, 7 August 2009
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	Here are frequently asked questions about ZINC.		Here are frequently asked questions about ZINC.

			* [[DOCK:FAQ]]
			* [[DUD:FAQ]]
			* [[DOCK Blaster:FAQ]]
			* [[THC:FAQ]]
			* [[FAQ]] for everything not covered by one of those products.

	Q1. I am trying to generate a subset of your "drug-like" molecule subset for		Q1. I am trying to generate a subset of your "drug-like" molecule subset for

Frodo at 22:28, 2 April 2009

2009-04-02T22:28:57Z

← Older revision		Revision as of 22:28, 2 April 2009
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	A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....		A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....
	[http://zinc.docking.org/scripts/get.db.from.id.sh].		[http://zinc.docking.org/scripts/get.db.from.id.sh].


			Here is how to use this script.

			First, put the ZINC IDs you want to get into a file, say "list1"

			Second, put the list of lists into a file, call this "masterlist"
			(i.e. line 1 of masterlist is contains 5 characters: list1

			Invoke the program

			chmod a+rx get.db.from.id.sh (as downloaded above)
			./get.db.from.id.sh masterlist 0 mol2 ; # to get "reference" molecules (0) in mol2 format
			./get.db.from.id.sh masterlist 1 mol2 ; # to get "additional physiological (mid, 1) in mol2

			Good luck!

Frodo at 19:36, 30 March 2009

2009-03-30T19:36:55Z

← Older revision		Revision as of 19:36, 30 March 2009
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			Q3. Is there a script that does all of this?

	~~Q3. Is there a script that does all of this?~~
	A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....		A3. Yes, Peter Kolb wrote one (thanks Peter). Download it here....
	[http://zinc.docking.org/scripts/get.db.from.id.sh].		[http://zinc.docking.org/scripts/get.db.from.id.sh].