ZINC26:Help - Revision history

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	~~This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.~~

	ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.		ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.

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	* Top level: Purchasable and Bioactive		* Top level: Purchasable and Bioactive
	* within purchasable:		* within purchasable:
	** ~~aristoInStock~~ - our preferred sources for inStock ~~compounds~~		** aristoStock - our preferred sources for inStock
	** ~~aristoOnDemand~~ - our preferred sources for onDemand ~~compounds~~		** aristoDemand - our preferred sources for onDemand
	** bBlocks - building blocks for synthesis		** bBlocks - building blocks for synthesis
	** commons - chemistry commons		** commons - chemistry commons
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	** inStock		** inStock
	** onDemand		** onDemand
	** Sundry
	* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)		* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

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	== More notes ==		== More notes ==

	Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.		* Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.
			* You must complete a captcha each time you open a new window to protect us from bots.
	We throttle usage in ~~other (so far undisclosed)~~ ways that allow us to offer a free public service without overloading.		* We throttle usage in various ways that allow us to offer a free public service without overloading.

	== Questions I can ask ==		== Questions I can ask ==
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	== Report Problems / Suggestions ==		== Report Problems / Suggestions ==
	* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9		* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
	* Send us catalogs that you do not see indexed.		* Send us catalogs that you do not see indexed.

			== Additional access with login ==
			If you login, you get extra access. This includes:
			* being able to search 10 SMILES at a time in batch instead of 1.
			* access to Arthor
			* access to Synthons

			== Work in progress ==
			We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search.



	[[Category:ZINC26]]		[[Category:ZINC26]]
	[[Category:JJI]]		[[Category:JJI]]

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2026-07-24T18:38:21Z

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← Older revision		Revision as of 18:38, 24 July 2026
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	ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.		ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.

	== Batch interface ==		== How to use the Interface ==

			=== Batch interface ===
	ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].		ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].

	== Interactive interface ==		=== Interactive interface ===
	ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.		ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.

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	** Sundry		** Sundry
	* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)		* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

			== Current Contents and Status of Databases ==
			* [[ZINC26:Databases]]

			== More notes ==

	Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.		Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.

	We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.		We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

			== Questions I can ask ==

	Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.		Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.
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	* what is the nearest metabolite to my compound?		* what is the nearest metabolite to my compound?
	* more to follow (food, etc)		* more to follow (food, etc)

	~~[[Category:ZINC26]]~~
	~~[[Category:JJI]]~~

	~~== When I search ZINC26 purchasable in batch, what am I really searching? ==~~

	* here is a page that describes what is currently searched [[ZINC26:Databases]]



	== Updates / Status ==		== Updates / Status ==
	* ~~As of July 2, 2026, zinc26 is in production at zinc26.docking.org.~~		* writing paper
	* We have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon-based libraries will be enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)		* checking everything
	* ~~We are aiming~~ to ~~offer~~ "~~all purchasable to HAC29" and "all bioactives~~" ~~as one-click interactive~~ databases~~. So far, we are not quite there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer.~~		* testing
	* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.		* we need to create/update the "All-" databases

	== ~~how to report suggestions~~ / ~~problems~~ ==		== Report Problems / Suggestions ==
	~~Please use~~ our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9		* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
			* Send us catalogs that you do not see indexed.
	* ~~Please send~~ us catalogs that you do not see indexed.

	[[Category:ZINC26]]		[[Category:ZINC26]]
			[[Category:JJI]]

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← Older revision		Revision as of 16:59, 24 July 2026
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	[[Category:ZINC26]]		[[Category:ZINC26]]
	[[Category:JJI]]		[[Category:JJI]]

			== When I search ZINC26 purchasable in batch, what am I really searching? ==

			* here is a page that describes what is currently searched [[ZINC26:Databases]]



	== Updates / Status ==		== Updates / Status ==

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	* what are the most similar molecules I can purchase?		* what are the most similar molecules I can purchase?
	* what the ~~most~~ most similar molecules I can purchase from a ~~particular~~ vendor (within a particular HAC range)?		* what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
	* Does vendor X sell compounds that look like my compound?		* Does vendor X even sell compounds that look like my compound?
	* what is the nearest drug to my compound?		* what is the nearest drug to my compound?
	* what is the nearest ~~chembl~~ bioactive 1uM or better to my compound?		* what is the nearest ChEMBL bioactive 1uM or better to my compound, and what target is it annotated for?
	* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?		* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
	* what is the nearest natural product to my compound?		* what is the nearest natural product to my compound?
	* what is the nearest metabolite to my compound?		* what is the nearest metabolite to my compound?
			* more to follow (food, etc)

			[[Category:ZINC26]]
			[[Category:JJI]]

	== Updates / Status ==		== Updates / Status ==

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2026-07-08T17:50:59Z

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← Older revision		Revision as of 17:50, 8 July 2026
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	ZINC26 ~~provides interfaces to search purchasable chemical space~~ and ~~biologically active chemical space~~.		This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.

	There are ~~two separate interfaces~~, ~~interactive (10s turnaround time)~~ and ~~batch (3 mins turnaround time if there is no queue)~~.		ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.

	The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each. ~~The batch interface searches _all_~~ purchasable ~~or _all_~~ bioactive ~~databases in a single transaction~~.		== Batch interface ==
			ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].

			== Interactive interface ==
			ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.

			== Organization ==
			* Top level: Purchasable and Bioactive
			* within purchasable:
			** aristoInStock - our preferred sources for inStock compounds
			** aristoOnDemand - our preferred sources for onDemand compounds
			** bBlocks - building blocks for synthesis
			** commons - chemistry commons
			** covalent - covalent
			** inStock
			** onDemand
			** Sundry
			* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

	Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.		Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.
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	== Updates / Status ==		== Updates / Status ==
	* As of July 2, 2026, zinc26 is in production at zinc26.docking.org ~~and zinc26dev.docking.org. If you cannot get in, write us at jjiteam at googlegroups dot com for access~~.		* As of July 2, 2026, zinc26 is in production at zinc26.docking.org.
	* we have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon based libraries will enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)		* We have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon-based libraries will be enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
	* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not ~~quiet~~ there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer		* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quite there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer.
	* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.		* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

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	* Please send us catalogs that you do not see indexed.		* Please send us catalogs that you do not see indexed.







	[[Category:ZINC26]]		[[Category:ZINC26]]

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2026-07-02T18:16:40Z

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← Older revision		Revision as of 18:16, 2 July 2026
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	ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.		ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.

	~~The interface at zinc26.docking.org features both an~~ interactive ~~batch method to search. The interative approach allows near-instant~~ (~10s) ~~searches of individual databases of up to 5 billion molecules in each transaction. This allows "what~~ if~~" type searches of parts of chemical space, and based on individual vendors~~.		There are two separate interfaces, interactive (10s turnaround time) and batch (3 mins turnaround time if there is no queue).

	~~== Interactive ==~~		The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each. The batch interface searches _all_ purchasable or _all_ bioactive databases in a single transaction.

	~~== Batch ==~~		Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction.

			We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

			Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

			* what are the most similar molecules I can purchase?
			* what the most most similar molecules I can purchase from a particular vendor (within a particular HAC range)?
			* Does vendor X sell compounds that look like my compound?
			* what is the nearest drug to my compound?
			* what is the nearest chembl bioactive 1uM or better to my compound?
			* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
			* what is the nearest natural product to my compound?
			* what is the nearest metabolite to my compound?

	~~== Searching Bioactive chemical space ==~~

	== Updates / Status ==		== Updates / Status ==
			* As of July 2, 2026, zinc26 is in production at zinc26.docking.org and zinc26dev.docking.org. If you cannot get in, write us at jjiteam at googlegroups dot com for access.
			* we have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon based libraries will enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
			* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quiet there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer
			* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

	== how to report suggestions / problems ==		== how to report suggestions / problems ==
			Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

			* Please send us catalogs that you do not see indexed.

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2026-06-16T18:59:06Z

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← Older revision		Revision as of 18:59, 16 June 2026
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	== ~~Introduction~~ ==		ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.
	~~For John Irwin~~ to ~~fill out~~
			The interface at zinc26.docking.org features both an interactive batch method to search. The interative approach allows near-instant (~10s) searches of individual databases of up to 5 billion molecules in each transaction. This allows "what if" type searches of parts of chemical space, and based on individual vendors.

			== Interactive ==

			== Batch ==

			== Searching Bioactive chemical space ==

			== Updates / Status ==

			== how to report suggestions / problems ==





			[[Category:ZINC26]]

Jgutierrez6: Created page with "== Introduction == For John Irwin to fill out"

2026-06-15T23:32:52Z

Created page with "== Introduction == For John Irwin to fill out"

New page

== Introduction ==
For John Irwin to fill out