ZINC15:examples: Difference between revisions

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== From the abstract ==
== From the abstract ==
[[ZINC15:examples:abstract]]
[[ZINC15:examples:abstract]]


== From the introduction ==
== From the introduction ==
[[ZINC15:examples:introduction]]
[[ZINC15:examples:introduction]]


== From the Results ==
== From the Results ==
Line 17: Line 15:


[[ZINC15-examples:results-text]]
[[ZINC15-examples:results-text]]






  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
  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 ==




Revision as of 20:34, 25 March 2015

Examples from the paper

From the abstract

ZINC15:examples:abstract

From the introduction

ZINC15:examples:introduction

From the Results

ZINC15:examples:results-tables

ZINC15:examples:results-figures

ZINC15-examples:results-text 


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


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

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