ZINC15:examples
Examples from the paper
From the abstract
From the introduction
From the Results
ZINC15:examples:results-tables
ZINC15:examples:results-figures
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