ZINC15:examples: Difference between revisions

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= Introduction =
= Introduction =
Here are examples of what you can do with ZINC15, organized by
Here are examples of what you can do with ZINC15, organized by [[ZINC15:Levels]].
* a) whether our solution is web accessible (public) or requires ssh access (private)
and
* b) level of difficulty - see [[ZINC15:Levels]] for difficulty levels.


= Public Access =
= Public Access =
Line 15: Line 12:
These require ssh access or a private copy of ZINC
These require ssh access or a private copy of ZINC
* [[ZINC15:examples:private]]
* [[ZINC15:examples:private]]
= 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;
Get supplier_codes for chembl20 compounds that match PAINS
wget -O- 'http://zinc15.docking.org/catalogs/chembl20/substances.json:zinc_id+catalog_items+patterns?patterns-any-origin_name=pains&count=all' | jq -r '[.zinc_id, (.patterns[] | select(.origin_name == "pains") | .name), (.catalog_items[] | select(.catalog_short_name == "chembl20") | .supplier_code)] | @csv' | csv --to-tsv | tee chembl-patterns.txt
= substance-oriented =
= gene-oriented =
Compounds that are similar to dopamine and are endogenous human metabolites
http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc(c(cc1CC[NH2])O)O
OR
http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=33882
Similar to (drug) and has been in man
http://zinc15.docking.org/substances/subsets/in-man.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc2c(cc1O)C[C@H](CC2)N
http://zinc15.docking.org/genes
list of genes and their major classes
http://zinc15.docking.org/genes/txt:name%2Cdescription%2Ctarget_class.name%2Ctarget_class.major_target_class.name/
list of target classes
http://zinc15.docking.org/targetclasses.txt:name
list of major target classes
http://zinc15.docking.org/majorclasses.txt:name
enzyme genes
http://zinc15.docking.org/genes.txt:name%2Cdescription+target_class.name?majorclass.name=enzyme
http://zinc15.docking.org/targets.txt:gene.name+majorclass.name%20eq%20enzyme
what it does
.../substance.structure similarto c1ccccc1CCCOC within .7 using tanimoto
blah
/substance/txt:zinc_id/substance isa metabolite
asdfasdf
/substances/txt:zinc_id?sort=substance.structure+near+c1ccccc1CCNC+using+dice
The organism table (modified from ChEMBL)
http://zinc15.docking.org/organisms/txt:organism_id,code,description/
Table of Dopamine receptor genes
http://zinc15.docking.org/targets.txt:name,description,gene.description,uniprot,chembl,gene_fk,gene.name?gene.name-startswith=DRD
List of chemotype clusters (not too useful, but proof of concept)
http://zinc15.docking.org/clusters.txt:number+gene.name
All compound-target pairs with activity of 1nM or better
http://zinc15.docking.org/activities.txt:substance.zinc_id+substance.best_purchasability+substance.best_catalog+target.name+affinitynm?activity.affinitynm-gt=9
Search by inchikey prefix
translator:
http://zinc15.docking.org/apps/mol/convert?from=c1ccccc1&to=inchikey
blah
http://zinc15.docking.org/substances?references-any-pubmed_id=14695814
http://zinc15.docking.org/substances/?inchikey-startswith=LFQSCWFLJHTTHZ
Search by inchikey
http://zinc15.docking.org/substances/?inchikey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Endogenous and Drug metabolites (ZINC, a new method to find problems in other databases)
http://zinc15.docking.org/catalogs/hmdbendo/substances/?catalogs-any-short_name=hmdbdrug
FDA approved but not in drugstore, generally this is due to stereochemistry issues in drugbank.
http://zinc15.docking.org/catalogs/dbfda/substances/?~catalogs-any-short_name=drugstore
first one: http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb
second one: (correct): http://zinc15.docking.org/catalogs/lipid/substances/?catalogs-any-short_name=lipid
blah
http://zinc15.docking.org/catalogs/foodb/substances/subsets/endogenous
Question: what compounds are in the "lipidomics" catalog but are NOT
in HMDB (as we currently have it loaded):
http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb
thus, compounds sold by sigma aldrich that hit DRD2 and not HRH1 pace ChEMBL,10uM.
http://zinc15.docking.org/catalogs/sial/substances/?genes-any-name=DRD2&~genes-any-name=HRH1
Only one catalog, and it is sial:
http://zinc15.docking.org/catalogs/sial/substances/?~catalogs-any-short_name-ne=sial
We would like a variant for no other catalog of type 50,40,20,10 only.  That's a request.
Metabolites that look like ethanol:
http://zinc15.docking.org/substances/subsets/metabolites/?ecfp4_fp-tanimoto-50=CCO
(produced in the gut by the bacterial flora)
Get fingerprint
http://zinc15.docking.org/substances/ZINC000018011573.txt:ecfp4_fp.as_base64
How many molecules are in pubchem?
http://zinc15.docking.org/catalogs/pubchem/substances?special=count
blah
http://zinc15.docking.org/catalogs/pubchem/substances?special=count-wait
blah
http://zinc15.docking.org/majorclasses/?substances-any-purchasability=for-sale
blah
http://zinc15.docking.org/majorclasses/?substances-any-purchasability=not-for-sale
blah
http://zinc15.docking.org/majorclasses/?substances-memberof=biogenic


[[Category:Tutorials]]
[[Category:Tutorials]]
[[Category:ZINC15]]
[[Category:ZINC15]]
[[Category:Idioms]]
[[Category:Idioms]]

Revision as of 23:46, 1 October 2015

Introduction

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

Public Access

Private access

These require ssh access or a private copy of ZINC

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