ZINC15:examples: Difference between revisions

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= Introduction =
Here are examples of what you can do with ZINC15, organized by [[ZINC15:Levels]].


= Examples from the paper =  
= Public Access =
* [[ZINC15:examples:public]]
* [[ZINC15:videos]]
* [[ZINC15:examples:screening]]


== From the introduction ==
query ZINC using api
1) “What is the nearest metabolite or drug to my compound?”
time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?
purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" | tee 18.txt | cat -n


2) “Which FDA approved drugs are also metabolites?”


3) “Which compounds are in Drugbank but not in ChEMBL Drugstore?”
= Private access =
These require ssh access or a private copy of ZINC
* [[ZINC15:examples:private]]


4) “Which genes have a ligand reported that binds at 10nM concentration or better?"
[[Category:Tutorials]]
 
5) “Which targets do hydroxamic acids bind to?”
 
6) “Which vendors sell the most biogenic compounds (natural products), and what are those compounds?”
 
7) “How many primary amines as for sale in preparative quantitites?”
 
== From Results ==
 
== Table 2 - Genes, Uniprot codes and annotated compounds by affinity bin ==
(re-write these as webapi)
* * 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 ==
(re-write these as ZINCAPI if we can)
 
* * 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;
 
 
== Table 7 - What genes do warheads hit? ==
compounds:
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/structure%20contains%20CS(=O)(=O)[ND1]&substance.purchasability%20gt%209
 
 
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20C(=O)[ND2][OD1]
3
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20cC(=O)[OD1]
4
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20CC(=O)[OD1]
5.
takes too long. Why for only 100?
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20[SH]
 
 
 
== Table 8A ==
 
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.
 
 
== 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.
 
 
 
 
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/gene.name%20eq%20DRD2&ecfp4.data%20similarto%20c1cc2c(cc1O)[C@H](CC2)Cc3c[nH]cn3%20within%200.39?count=all
 
== 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 ==
 
 
 
 
 
 
== Molecular features ==
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/structure contains
 
here another
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,best_purchasable/substance.features%20contains%20201,&catalog.purchasable gt 9?count=all. 
 
and another
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,best_purchasable/substance.features%20contains%20216,&catalog.purchasable gt 9?count=all. 
 
available features
http://zincapi.ucsf.bkslab.org/v1/features/txt:feature_id%2Cdescription%2Crecipe/. (supporting information).   
 
another one
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20201,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5%20using%20tanitmoto 
 
 
and another:
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20201,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all. 
 
and another
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20213,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all
 
 
 
 
 
For instance, to look up the drug aripiprazole by its InChI use
zinc15.docking.org/substances?inchi=InChI=1S/C23H27Cl2N3O2/c24-19-4-3-5-21(23(19)25)28-13-11-27(12-14-28)10-1-2-15-30-18-8-6-17-7-9-22(29)26-20(17)16-18/h3-6,8,16H,1-2,7,9-15H2,(H,26,29).
 
To look it (aripiprazole) up by its InChIkey, use
zinc15.docking.org/substances?inchikey=CEUORZQYGODEFX-UHFFFAOYSA-N
 
To look up molecules that share the same molecular framework of aripiprazole, use
zinc15.docking.org/substances?inchikey=CEUORZQYGODEFX%
 
Whereas InChI and InChIkeys are increasingly widely available, an InChI to SMILES translator is available to help facilitate the transition at:
zinc15.docking.org/actions/translate
 
 
= 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
 
== orphan ==
 
 
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
 
 
= Website Main entry points =
 
== Browse all compounds in ZINC ==
http://zinc15.docking.org/substances
Variant 1: all in-stock compounds, as SMILES
http://zinc15.docking.org/substances.smi/in-stock
Variant 2: all biogenic building blocks sold by Sigma Aldrich, as an Excel spreadsheet
http://zinc15.docking.org/substances.xlsx?catalog.name=sialbb&catalog.np=1
 
== Browse all vendors in ZINC ==
http://zinc15.docking.org/catalogs
Variant 1:
http://zinc15.docking.org/catalogs
Variant 2:
http://zinc15.docking.org/catalogs
 
== Browse all genes in ZINC ==
http://zinc15.docking.org/catalogs
Variant 1: eukaryotic genes
http://zinc15.docking.org/catalogs?organism.name=Eukaryotic
Variant 2: genes for eukaryotic transporters
http://zinc15.docking.org/catalogs?major_class.name='transporter'&organism.type=E
 
== Browse all target classes in ZINC ==
http://zinc15.docking.org/target_classes
Variant 1: eukaryotic genes
http://zinc15.docking.org/catalogs?organism.name=Eukaryotic
Variant 2: genes for eukaryotic transporters
http://zinc15.docking.org/catalogs?major_class.name='transporter'&organism.type=E
 
 
== List options ==
Wait, what are the available major classes?
  http://zinc15.docking.org/majorclasses
And the available organism types?
http://zinc15.docking.org/organisms
 
Back to [[Webapi]]
[[Category:ZINC15]]
[[Category:ZINC15]]
[[Category:Idioms]]

Latest revision as of 17:34, 17 August 2017

Introduction

Here are examples of what you can do with ZINC15, organized by ZINC15:Levels.

Public Access

query ZINC using api 

time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?
purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" | tee 18.txt | cat -n


Private access

These require ssh access or a private copy of ZINC

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