ZINC15:examples

Examples organized by topic

purchasable screening libraries

ZINC15:examples:screening

Examples organized by level of difficulty

See ZINC15:Levels for a description of our classification of questions by how easy it is to answer them.

Public access

• ZINC15:examples:level1 - questions that are easy to answer using the [zinc15.docking.org zinc15.docking.org] web page.
• ZINC15:examples:level2 - questions that require you compose your own query in the URL. This is usually because we have not yet gotten around to writing a graphical interface for this class of questions.
• ZINC15:examples:level3 - these are questions that are difficult or not possible to answer using the ZINC 15 website as it currently exists, but can be answered using a bit of python. We show you how. Using a bit of python can dramatically extend the power of the ZINC website.

Private access required

• ZINC15:examples:level4 - these (and all higher levels) require privileged access to ZINC which is not available to the general public. However, by showing you what these questions are, and how you can solve them with access, we alert you to the possibilities of ZINC. Ask us if you require this level of access to ZINC.
• ZINC15:examples:level5 - higher level access. not just privileged ipynb, but also command line ZINC shell.
• ZINC15:examples:level6 - SQL
• ZINC15:examples:level7 - SQL and python
• ZINC15:examples:level8 - questions we've been asked that we are unable to answer as this time.

zinc15.docking.org/substances.txt:smiles,zinc_id,tanimoto_similarity? 
catalog.purchasable%20gt%209&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all

YouTube

iPython Notebooks

How many primary amines are available for sale in preparative quantities?

URL="zinc15.docking.org:8015/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&substance.purchasability:gt=9&count=all"
wget -o log -O amines.smi "$URL"
wc -l amines.smi

answer: xxxx

How many ChEMBL targets have at least one purchasable compound for sale?

zinc15.docking.org:8015/activities:target.uniprot?catalog.purchasable .....

How many ligands for class F GPCRs are for sale?

zinc15.docking.org:8015/substances.txt:smiles,sub_id,gene.name?subclass=name=GPCR-F&substance.purchasability:ge=10&count=all

What is the nearest metabolite or drug to my compound?

zinc15.docking.org/substances.txt?ecfp4.data:tanimoto,0.5=<url-encoded-smiles>

thus for ZINC27,

zinc15.docking.org/substances.txt?ecfp4.data:tanimoto,0.5=N[C@@H](CCc1ccc(N(CCCl)CCCl)cc1)C(=O)O

Which FDA approved drugs are also metabolites?

zinc15.docking.org/substances?substance.features:contains=211,202&count=all

Which genes have a ligand reported that binds at 10nM concentration or better?

zinc15.docking.org:8015/activities.txt:gene.name?activities.affinitynm:ge=8&distinct=gene.name&count=all

Which targets do hydroxamic acids bind to?

zinc15.docking.org/targets.txt:target.uniprot?structure.contains=C(=O)[ND2][OD1]&distinct=target.uniprot&count=all

Which vendors sell the most biogenic compounds (natural products), and what are those compounds?

zinc15.docking.org/catitms.txt:catalog.short_name,catitm.supplier_code,substance.zinc_id,substance.smiles?catalog.np=1&count=all

How many primary amines as for sale in preparative quantitites?

zinc15.docking.org/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&count=all