View source for ZINC15:examples

{{TOCright}}
This continues to be an aspirational document, but we really are working on it!

Examples organized by public/private and level of difficulty ==
See [[ZINC15:Levels]] for a description of our classification of questions by how easy it is to answer them.
Please see also [[ZINC15:videos]] for discussions of various topics.
Please also see [[ZINC15:examples:screening]]  and   [[ZINC15:examples:resources]] for more examples.

= Public Access =
== Level 1 questions - easy to answer using webpage ==
Ligands for Dopamine D2 receptor:
 http://zinc15.docking.org/genes/DRD2/substances

All available genes
 http://zinc15.docking.org/genes

How many ChEMBL targets have at least one purchasable compound for sale?
 zinc15.docking.org/activities:target.uniprot?catalog.purchasable .....

How many ligands for class F GPCRs are for sale?
 zinc15.docking.org/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 compounds are in Drugbank but not in ChEMBL Drugstore?

Which genes have a ligand reported that binds at 10nM concentration or better?
 zinc15.docking.org/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

World drugs with no gene target annotated and no SEA prediction
 http://zinc15.docking.org/substances/subsets/world/having/no-genes+no-predictions/

In-man compounds having no annotations in ChEMBL but DO have SEA predictions
 http://zinc15.docking.org/substances/subsets/in-man/having/no-genes+predictions/

World drugs having no annotations, 10uM or better
 http://zinc15.docking.org/substances/subsets/world/having/no-genes/

World drugs containing indole and having no genes annotated:
 http://zinc15.docking.org/rings/indole/substances/subsets/world/having/no-genes/

World drugs having one or more PAINS patterns:
 http://zinc15.docking.org/substances/subsets/world/having/patterns/subsets/pains/?sort=no

Aggregators that have been in clinical trials:
 http://zinc15.docking.org/substances/subsets/aggregators/having/trials/

Endogenous human metabolites that have PAINS patterns (lots of incorrectly curated, please tell the source databases)
 http://zinc15.docking.org/substances/subsets/endogenous/having/patterns/subsets/pains/?sort=no 

Compounds of biological origin that are also FDA approved drugs:
 http://zinc15.docking.org/substances/subsets/fda+biogenic/

Biogenic compounds that hit phosphatase targets
 http://zinc15.docking.org/subclasses/phosphatase/substances/subsets/biogenic/

Biogenic compounds that hit a GPCR-A target and are predicted for one or more ion channels using SEA:
 http://zinc15.docking.org/substances/subsets/biogenic/?genes-any-sub_class_name=GPCR-A&predictions-any-major_class_name=ion%20channel

Metabolites that are annotated for annotated for both GPCR Class A and for one or more ion channels:
 http://zinc15.docking.org/substances/subsets/metabolites/?genes-any-sub_class_name=GPCR-A&genes-any-major_class_name=ion%20channel

Compounds of biological origin have 3-ring systems:
 http://zinc15.docking.org/substances/subsets/biogenic/having/rings/subsets/triple/

All individual species-specific targets for the MCHR2 gene:
 http://zinc15.docking.org/genes/MCHR2/targets/

Compounds that are world drugs and natural products:
 http://zinc15.docking.org/substances/subsets/world+natural-products/

Genes that have no compounds annotated for them at 1uM or better and are also for sale. 
 http://zinc15.docking.org/genes/having/no-activities/subsets/1uM/?related.purchasability=for-sale&num_substances-ge=1

Purchasable compounds for the APLNR gene in listing format:
 http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/table.html

Purchasable compounds for the delta opioid receptor OPRD1 in tile format:
 http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/

GPCR Class A genes with no compounds active at 100nM or better:
 http://zinc15.docking.org/genes/subsets/gpcra/having/no-activities/subsets/100nM/?num_substances-ge=1

GPCR Class F genes with no compound active at 1uM or better:
 http://zinc15.docking.org/genes/subsets/gpcrf/having/no-activities/subsets/1uM/

5HT ligands, colored by endogenous ligand
 http://zinc15.docking.org/genes/HTR1D/substances/?highlight=5-HT&ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12
and sorted by affinity....
 http://zinc15.docking.org/genes/HTR1D/activities/?highlight=5-HT&substance.ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12

== Level 2 questions - edit URL by hand ==
This is usually because we have not yet gotten around to writing a graphical interface for this class of questions. 

Description
 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

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

== Table 6 ==

1 compounds:
 http://zinc15.docking.org/substances.txt:smiles,zinc_id?structure-contains=CS(=O)(=O)[ND1]&substance.purchasability=for-sale

genes: 2
 http://zinc15.docking.org/substances.txt:smiles,zinc_id?substance.purchasability=for-sale&structure-contains=C(=O)[ND2][OD1]

3
 http://zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=cC(=O)[OD1]

4
 zinc15.docking.org/v1/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=CC(=O)[OD1]

5.
 zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=[SH]&count=all


6.  Primary amines.

== Table 7 - What genes do warheads hit? ==
compounds:
1
 zinc15.docking.org/substances.txt:smiles,zinc_id?structure-contains=CS(=O)(=O)[ND1]&purchasability=for-sale
2
 zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=C(=O)[ND2][OD1]

3
 zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=cC(=O)

4
 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20CC(=O)[OD1]
5.

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20[SH]

 1.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20201,
 2.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20202,
 3.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20203,

 &substance.purchasability >20 =20, =10, >1.

== Level 3 questions - not possible in one line - requires python == 
Using a bit of python can dramatically extend the power of the ZINC website.

= Private access required =

== Level 4 - privileged access == 
Ask us if you require this level of access to ZINC.

== Level 5 - command line ZINC shell ==

== Level 6 - SQL ==

How to calculate results from the ZINC15 2015 paper:

Table 2 - Genes, Uniprot codes and annotated compounds by affinity bin ==

* * select organism_fk, count(gene_id) from gene group by organism_fk;
 zinc15.docking.org/genes.txt:count(*)?group-by=organism_fk

* + select g.organism_fk, count(a.anno_id) from annotation a, gene g where a.gene_fk = g.gene_id group by g.organism_fk;
 zinc15.docking.org/targets.txt:count(*)?group-by=gene.organism_fk

* $ select count(distinct(n.sub_id_fk)),g.organism_fk from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 9 group by g.organism_fk;
 zinc15.docking.org/  not sure we can do this!

Table 3 - Gene Target Classes

* * select count(g.gene_id),tc.major_class from target_class tc, gene g where g.target_class_fk = tc.target_class_id group by tc.major_class order by tc.major_class

* + select count(distinct(s.sub_id)),tc.major_class from gene g, substance s, note n, annotation a, target_class tc where g.gene_id = a.gene_fk and g.target_class_fk = tc.target_class_id and n.anno_id_fk = a.anno_id and s.sub_id = n.sub_id_fk and s.purchasability >20, 20, 10 group by tc.major_class

* $ select count(distinct(g.gene_id)), tc.major_class from target_class tc, gene g, substance s, note n, annotation a where s.sub_id = n.sub_id_fk and a.anno_id = n.anno_id_fk and a.gene_fk = g.gene_id and  g.target_class_fk = tc.target_class_id and s.purchasability > 9 group by tc.major_class;

Table 4 - Chemical Diversity by Gene

4) histogram of clusters per gene.
 select c.gene_fk, g.name, count(c.cluster_id) from cluster c, gene g where g.gene_id = c.gene_fk and c.ordinal = 1 group by c.gene_fk,g.name order by count(c.cluster_id) desc;

for any one pick the smiles:
 select smiles,sub_id from substance where sub_id in (select rep_sub_id_fk from cluster where gene_fk = 57387 and ordinal=1);

another
 select c.gene_fk, g.name, count(c.cluster_id) from cluster c, gene g where g.gene_id = c.gene_fk and c.ordinal = 1 group by c.gene_fk,g.name order by count(c.cluster_id) desc;

another
 select gene_fk, count(cluster_id) from cluster where ordinal = 1 group by gene_fk order by count(cluster_id) desc ;


Table 5 - Genes per compound as a function of affinity cutoff (polypharmacology) 
this is almost for sure wrong:

 select sub_id  count(sub_id_fk) from note as n join annotation as a on n.anno_id_fk = a.anno_id join gene as g on g.gene_id = a.gene_fk group by n.sub_id_fk having min(n.affinitynM) >= 9;

NEW

Non purch:
 select count(sub_id_fk) as num_compounds, cgi as having_num_genes from (select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 9 group by n.sub_id_fk) as t group by cgi order by cgi;

Heavy hitters:
 select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 9 group by n.sub_id_fk order by cgi desc limit 10;

Purch:
 select count(sub_id_fk) as num_compounds, cgi as having_num_genes from (select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and c.purchasable>9 group by n.sub_id_fk) as t group by cgi order by cgi;

Heavy hitters (purch):
 select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and c.purchasable>9 group by n.sub_id_fk

== Level 7 - Python+SQL ==

== Level 8 - Questions we cannot answer (yet) ==


= Examples mentioned in or implied by the 2015 paper = 

== NEW TABLE 8 ==
chemical warheads and the genes they hit as a function of affinity.
 http://zincapi.ucsf.bkslab.org/v1/activities/txt:target.gene.name,substance.smiles,substance.zinc_id,substance.purchasability/activity.affinitynm ge 7&substance.structure%20contains%20cC(=O)[OD1]?count=all

== Table 8B == 

 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20211,
 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20212,
 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20213,
&substance.purchasability >20 =20, =10, >1. 

== Figure 1 ==
Drawn. probably to delete.

== Figure 2 == 

Non-purch final:
 psql -h samekh -U test zinc15 -c "select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 1 group by g.name " > 1-10um.txt

Purch final:
 psql -h samekh -U test zinc15 -c "select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 2 and c.purchasable > 9  group by g.name" > 2-10um-purch.txt

Unknown
 http://api.docking.org/v1/activities/txt:target.gene.name,sub_id_fk,affinitynm,substance.best_purchasbility

New non-purch
 select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 6 and g.organism_fk = 1 group by g.name; (by organism x 4)

Purch:
 select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and g.organism_fk = 2 and c.purchasable > 9  group by g.name  limit 10;

== Figure 3 == 


== Actions == 

Translate
 zinc15.docking.org/actions/translate

Nearest Metabolite
 zinc15.docking.org/actions/translate

Build dockable library
 zinc15.docking.org/actions/build-library

One-step reactions
 zinc15.docking.org/actions/reaction

 alter user zincfree set search_path = "$user", free, public;


 

[[Category:ZINC15]]