ZINC26:Help: Difference between revisions

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ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.  
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.


There are two separate interfaces, interactive (10s turnaround time) and batch (3 mins turnaround time if there is no queue).
== Database Organization == 
In both the interactive and batch interfaces, the top level categories are:


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.  
* [[ZINC26:Bioactive Databases]] - molecules with reported biological activity
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.
* [[ZINC26:Catalogs:Synthons]] -  reagents you can buy


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.
* [[ZINC26:Databases]]
* [[ZINC26:Progress]]


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


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


* what are the most similar molecules I can purchase?
{| class="wikitable"
* 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?
! Batch Category !! # files !! size !! Catalogs
* what is the nearest drug to my compound?
|-
* what is the nearest chembl bioactive 1uM or better to my compound?
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi,
* 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?
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP
* what is the nearest metabolite to my compound?
|-
|}


=== 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.


== Updates / Status ==  
=== The API ===  
* 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.
Description here.
* 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 ==  
== Levels of Access and Limitations ==  
Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9


* Please send us catalogs that you do not see indexed.  
* There are four levels of access.
* anonymous users - no login required. One molecule at a time in batch.
** All Smallworld databases are visibile, but only small Arthor databases are visible.
 
* authenticated users - more privileges. Ten molecules at a time in batch.
** All Arthor databases are visible, but there is a time limit on searches.  


* UCSF users - more access for folks in our research group.
** Higher limits required for our own research and testing


== Questions I can ask ==
[[ZINC26:Questions]]


== 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.






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

Latest revision as of 17:41, 2 October 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.

Database Organization

In both the interactive and batch interfaces, the top level categories are:

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.

Batch Category # files size Catalogs
Purchasable 51 300B Enamine REAL, ChemSpace FS5, WuXi GalaXi,
Bioactive 3 1M Drugbank, ChEMBL 1uM, Coconut, other NP

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.

The API

Description here.

Levels of Access and Limitations

  • There are four levels of access.
  • anonymous users - no login required. One molecule at a time in batch.
    • All Smallworld databases are visibile, but only small Arthor databases are visible.
  • authenticated users - more privileges. Ten molecules at a time in batch.
    • All Arthor databases are visible, but there is a time limit on searches.
  • UCSF users - more access for folks in our research group.
    • Higher limits required for our own research and testing

Questions I can ask

ZINC26:Questions

Updates / Status

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

Report Problems / Suggestions

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