ZINC26:Help: Difference between revisions

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:

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

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

Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
Send us catalogs that you do not see indexed.

@@ Line 1: / Line 1: @@
 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:
+* [[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
+* [[ZINC26:Databases]]
+* [[ZINC26:Progress]]
 == How to use the Interface ==
@@ Line 5: / Line 16: @@
 === 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]].
+{| class="wikitable"
+|-
+! 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.
-[[ZINC26:Organization]]
+=== The API ===
+Description here.
+== Levels of Access and Limitations ==
-== Current Contents and Status of Databases ==
+* There are four levels of access.
-* [[ZINC26:Databases]]
+* anonymous users - no login required. One molecule at a time in batch.
-* [[ZINC26:Purchasable Databases]]
+** All Smallworld databases are visibile, but only small Arthor databases are visible.
-* [[ZINC26:Bioactive Databases]]
-* [[ZINC26:Special Databases]]
+* authenticated users - more privileges. Ten molecules at a time in batch.
-* [[ZINC26:Progress]]
+** All Arthor databases are visible, but there is a time limit on searches.
-== More notes ==
+* UCSF users - more access for folks in our research group.
+** Higher limits required for our own research and testing
-* 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 ==
@@ Line 37: / Line 57: @@
 * 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
-== 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.