ZINC26:Help: Difference between revisions

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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.
== How to use the Interface ==


== Batch 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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* 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
Line 19: Line 19:
** 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)


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.  
== 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.
* You must complete a captcha each time you open a new window to protect us from bots.
* We throttle usage in various 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.  


* 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)
 
== Updates / Status ==
* writing paper
* checking everything
* testing
* we need to create/update the "All-" databases
 
== Report Problems / Suggestions ==
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
* 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


== Updates / Status ==  
== Work in progress ==
* As of July 2, 2026, zinc26 is in production at zinc26.docking.org.
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.  
* 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 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.  


== 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.


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

Latest revision as of 05:07, 27 July 2026

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.

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.

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:
    • aristoStock - our preferred sources for inStock
    • aristoDemand - our preferred sources for onDemand
    • bBlocks - building blocks for synthesis
    • commons - chemistry commons
    • covalent - covalent
    • inStock
    • onDemand
  • within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

Current Contents and Status of 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.
  • You must complete a captcha each time you open a new window to protect us from bots.
  • We throttle usage in various 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.

  • what are the most similar molecules I can purchase?
  • what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
  • Does vendor X even 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, 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 natural product to my compound?
  • what is the nearest metabolite to my compound?
  • more to follow (food, etc)

Updates / Status

  • writing paper
  • checking everything
  • testing
  • we need to create/update the "All-" databases

Report Problems / Suggestions

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.

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