Chemical libraries

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 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 and, especially, ZINC 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 and representative compound libraries that we offer as default search libraries in the Chemical Checker similarity resource.

• Approved Drugs apd: https://www.drugbank.ca/. Approved drugs according to DrugBank.
• Experimental Drugs exd: https://www.drugbank.ca/. Experimental drugs according to DrugBank. We remove drugs that are considered to be approved.
• Human Metabolites hmbdb: http://www.hmdb.ca/. Human metabolites available from the Human Metabolome Database.
• Traditional Chinese Medicines tcm: http://tcm.cmu.edu.tw/. Traditional Chinese Medicines from TCM@Taiwan database. This is the world's largest collection of Chinese medicines.
• LINCS Compounds lincs: http://lincsportal.ccs.miami.edu/SmallMolecules/. Compounds, mainly from the Broad Institute Library, related to the LINCS consortium.
• Prestwick Chemical Library prestw: http://www.prestwickchemical.com/libraries-screening-lib-pcl.html. A commercial collection of over 1.2k off-patent drugs.
• 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

We have a particular interest in natural product (NP) databases, mainly because they are likely to be useful for Global Health research.

• South African Natural Compounds Database (SANCDB): 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: Dataset 1 in Ntie-Kang et al. 2013. Contains 947 compounds. Coordinated from Cameroon.

• Natural Product Activity and Species Source database (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/. About 4.5k NPs from Northern Africa, mainly from plants.

• Brazilian Natural Compound Database (NUBBEdb): https://nubbe.iq.unesp.br/portal/nubbedb.html. Contains 640 molecules mainly from plants in Brazil.