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# Chemical libraries
The following is a list of chemical libraries that may be used in virtual screening scenarios.
The following is a list of chemical libraries that we like to use in virtual screening exercises.
* In the SB&NB file-system, compound collections can be found in `/aloy/web_checker/libraries/`.
* The `chemical_checker` [PostGreSQL database](database) contains the compound collections, too, in the `libraries` table.
These are only a very small selection of compound collections. The best way to browse compound collections is via [ZINC Subsets](http://zinc15.docking.org/substances/subsets/) and, especially, [ZINC Catalogs](http://zinc15.docking.org/catalogs/). ZINC assigns an `abbreviation` to every collections, and we stick with this notation as long as the database is indeed present in ZINC.
## Exemplar collections
These are popular compound libraries that we offer as default search libraries in the [Chemical Checker similarity resource](http://www.chemicalchecker.org).
These are popular and representative compound libraries that we offer as default search libraries in the [Chemical Checker similarity resource](http://www.chemicalchecker.org).
* Approved Drugs:
* Experimental Drugs:
* Human Metabolites:
* Traditional Chinese Medicines:
* LINCS Compounds:
* Prestwick Chemical Library:
* NIH Clinical Collection:
* NCI Diversity Collection:
* Tool Compounds:
* Approved Drugs `apd`:
* Experimental Drugs `exd`:
* Human Metabolites `hmet`:
* Traditional Chinese Medicines `tcm`:
* LINCS Compounds `lincs`:
* Prestwick Chemical Library `prestw`:
* NIH Clinical Collection `nihcc`:
* NCI Diversity Collection `ncidiv`:
* Tool Compounds `tool`:
## Screening libraries
*
There is a great number of chemogenomics databases that one may consider. I list here the ones selected in an important recent review on the matter: .
## Natural product databases
......@@ -29,19 +31,10 @@ We have a particular interest in natural product (NP) databases, mainly because
* South African Natural Compounds Database (SANCDB): [https://sancdb.rubi.ru.ac.za/](https://sancdb.rubi.ru.ac.za/). Contains about 600 NPs, all of them with some degree of bioactivity annotation. Belongs to the Research Unit in Bioinformatics (RUBi), NIH Common Fund and Rhodes University.
* AfroDB: [](). Contains 947 compounds. Coordinated from Cameroon.
* AfroDB: [Dataset 1 in Ntie-Kang et al. 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078085#s5). Contains 947 compounds. Coordinated from Cameroon.
* Natural Product Activity and Species Source database (NPASS): [http://bidd2.nus.edu.sg/NPASS/](http://bidd2.nus.edu.sg/NPASS/). Over 35k well-annotated compounds, belonging to 25k organisms.
* Northern African Natural Products Database (NANPDB): [http://african-compounds.org/nanpdb/](http://african-compounds.org/nanpdb/). About 4.5k NPs from Northern Africa, mainly from plants.
* Brazilian Natural Compound Database (NUBBEdb): [https://nubbe.iq.unesp.br/portal/nubbedb.html](https://nubbe.iq.unesp.br/portal/nubbedb.html).
*
NUBBEdb: Brazilian Natural Compound Database: https://nubbe.iq.unesp.br/portal/nubbedb.html
Traditional Chinese Medicine Database (TCM) . Based in Taiwan.
## Other databases
* Please consider [ZINC Subsets](http://zinc15.docking.org/substances/subsets/) and, especially, [ZINC Catalogs](http://zinc15.docking.org/catalogs/) for further search and to rapidly download compound structures as SMILES strings.
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* Brazilian Natural Compound Database (NUBBEdb): [https://nubbe.iq.unesp.br/portal/nubbedb.html](https://nubbe.iq.unesp.br/portal/nubbedb.html). Contains 640 molecules mainly from plants in Brazil.