Compounds.md

DrugAI

Compound libraries

Note: SDF file could be parsed by RDKit

1. Drugbank

   • API
   • Need to signup with your academic email, then you could download the molecules.
   • Clinical trial molecules (11,294) from DrugBank were used with the NASH stage III markers

2. PubChem

   • API
   • PubChemPy
   • SMILES representation for virtual screen (Bulk download): https://ftp.ncbi.nlm.nih.gov/pubchem
     • wget -r ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/
   • 3D structrue for virtual screen (Bulk download):
     • wet -r ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound_3D/01_conf_per_cmpd/SDF/
     • select 1 compound 1 3D structruture

3. ChEMBL : ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

   • chembl_29_chemreps.txt.gz
   • chembl_29.sdf.gz

4. HMDB :

   • Metabolite Structures
   • All metabolites

5. LIPID MAPS

   • LMSD
   • API access
   • As of 09/03/2021, LMSD contains 46150 unique lipid structures, making it the largest public lipid-only database in the world.

6. Metlin

   • 960,000 compounds
   • not available

7. TargetMol

   • Catalog No. L6000: Natural Compound Library for HTS
     • a unique collection of 2960 natural products with known bioactivity, wide source, and high cost effectiveness
   • Catalog No. L4200: FDA-approved Drug Library
     • 470 FDA approved drugs

8. others:

   • all kinds compounds are curated here, include targetmol
   • http://www2.sibcb.ac.cn/cp13-5_3.asp