ZINC26

Introduction

ZINC26 is a search tool for purchasable chemical space. It uses Smallworld and Arthor technology from NextMove Software to allow searching billions of molecules in seconds. There is a batch interface and an interactive one.

• help page: ZINC26:Help

The new database is organized around a set of principles.

API

• zinc26.docking.org/docs describes how to use. Here is a short tutorial to get you started using curl

SW search API

Step 1 : Check available databases/categories/catalogs

• Command

curl "https://zinc26.docking.org/sw/maps"

• Response:

{"Bioactive":
   {"inVitro":
     ["00chembl","mapsAADAC","mapsAADAT","mapsAAK1","mapsABAT"]
   }
}

Step 2 : Submit a search

• Command

curl "https://zinc26.docking.org/sw/search?database=Bioact&category=inVivo&catalog=dball&smiles=CCCCC&ced=4&ged=2&terminalUp=4&terminalDown=4&ringUp=2&ringDown=4&linkerUp=2&linkerDown=2&mutationMajor=4&mutationMinor=4&hybridisation=4&substitution=4&atomAlignment=true&multiSource=false"
 Required parameters:
   - database — e.g. Purchasable, Bioact
   - category — e.g. inVivo (from /sw/maps)
   - catalog — e.g. dball (from /sw/maps)
   - smiles — your query molecule in SMILES notation
 Optional distance parameters:
   - ced — chemical edit distance (0 to 4, default to 4)
   - ged — graph edit distance (0 to 2, default to 2)
   - terminalUp (0 to 8, default to 4)
   - terminalDown (0 to 8, default to 4)
   - ringUp (0 to 8, default to 2)
   - ringDown (0 to 8, default to 2)
   - linkerUp (0 to 8, default to 2)
   - linkerDown (0 to 8, default to 2)
   - mutationMajor (0 to 8, default to 4)
   - mutationMinor (0 to 8, default to 4)
   - hybridisation (0 to 8, default to 4)
   - substitution (0 to 8, default to 4)

• Response:

   {"task_id": "abc-123", "status": "PENDING"}

Step 3 : Check for results

• Command

curl "https://zinc26.docking.org/sw/result?task_id=abc-123"

• Response

Poll this until status is SUCCESS (or FAILURE). While running it may return PROGRESS with partial results:
  {
     "task_id": "abc-123",
     "status": "SUCCESS",
     "results": [...]
   }

Arthor search API

==== Step 1 : Check available database/category/catalog

• Command

curl "https://zinc26.docking.org/arthor/maps"

• Response:

{"Purchasable":
  {
   "bBlocks":
     ["bbA050","bbA100","bbA250","bbA500","bbA999","bbAFAS","bbAall"],
   "covalent":["acrylamides","activated_amides_ureas","activated_ureas","aldehydes","aminonitriles"],
   },
 }

Step 2 : Submit a search

Three search types are supported:

• Similarity search:

curl "https://zinc26.docking.org/arthor/searchtype=similarity&database=Bioact&category=inVivo&catalog=dball&query=CCO"

• Substructure search:

curl "https://zinc26.docking.org/arthor/search?type=substructure&database=Bioact&category=inVivo&catalog=dball&query=CCO&ringLocked=true&chainLocked=true&propertiesLocked=true"

• SMARTS search:

curl "https://zinc26.docking.org/arthor/search?type=smarts&database=Bioact&category=inVivo&catalog=dball&ringLocked=true&chainLocked=true&propertiesLocked=true"

Required parameters:
  - type — similarity, substructure, or smarts
  - database, category, catalog — from /arthor/maps
  - query — SMILES or SMARTS string (URL-encoded)
Optional (substructure/smarts only):
  - ringLocked — default true
  - chainLocked — default true
  - propertiesLocked — default true

• Response

{"task_id": "abc-123", "status": "PENDING"}

Step 3 : Check for results

• Command

curl "https://zinc26.docking.org/arthor/result?task_id=abc-123"

• Response

Poll until status is SUCCESS. While running you may get PROGRESS with partial results:
{
 "task_id": "abc-123",
 "status": "SUCCESS",
 "results": [...]
}

Batch Job search API

Step 1 : Login and get token

curl -X POST https://zinc26.docking.org/api/auth/login \
 -H "Content-Type: application/json" \
 -d '{"email": "you@example.com", "password": "yourpassword"}'

Step 2 : Submit a job

• Command Option A — JSON (molecules array, up to 10):

curl -X POST https://zinc26.docking.org/psp/submit \
 -H "Content-Type: application/json" \
 -d '{
   "token": "<your_token>",
   "db": "purchasable",
   "molecules": [
     {"smiles": "CCO", "compound_id": "mol1"},
     {"smiles": "c1ccccc1", "compound_id": "mol2"}
   ]
 }'

• Command Option B — File upload (.smi file, up to 10 molecules):

curl -X POST https://zinc26.docking.org/psp/submit \
 -F "token=<your_token>" \
 -F "db=purchasable" \
 -F "file=@molecules.smi"

Your .smi file should have one molecule per line space separated (SMILES compound_id):

CCO mol1
c1ccccc1 mol2

• Response:

{"job_id": "abc-123", "slurm_ids": [], "status": "QUEUED"}

Step 3 : Check job status

• Command

curl "https://zinc26.docking.org/psp/status?job_id=abc-123"

• Response

Poll until state is COMPLETED (or FAILED):
{
 "job_id": "abc-123",
 "state": "COMPLETED",
 "progress": {"completed": 2, "total": 2},
 "download_url": "/psp/download?job_id=abc-123"
}

Step 4: Download Results

• Command

curl "https://zinc26.docking.org/psp/download?job_id=abc-123" -o results.zip

Coming soon

• 3d database builder
• additional data

Tutorial in how to use datawarrior

• the columns in datawarrior are as follows.
• we are still working on adding a net_charge column.
• we suggest you proceed as follows.