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 Methods ==
 
 
== From Results ==
 
== From Discussion ==
 
 
 
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
 
 
we list as many as we can here, from the paper, with variants.
 
 
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
 
Wait, what are the available major classes?
  http://zinc15.docking.org/majorclasses
And the available organism types?
http://zinc15.docking.org/organisms
 
More...
 
 
 
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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