Introduction to PubChem

PubChem is a public chemical database maintained by the National Center for Biotechnology Information (NCBI). It contains:

• Millions of compounds (small molecules, peptides, lipids, etc.)

• Biological assay data (useful for drug discovery)

• Chemical properties (e.g., molecular weight, solubility, Lipinski’s Rule of Five compliance)

• 3D structures (essential for molecular docking) 

PubChem can be accessed through its website, PubChem. The interface allows searching for chemical compounds using various identifiers.

You can search PubChem using:

Chemical names (e.g., "aspirin")

SMILES/InChI (structural notations)

Molecular formula (e.g., "C9H8O4")

PubChem CID (unique identifier)

By drawing the chemical structure.

In computational drug discovery, a ligand library is a collection of small molecules (ligands) that are screened against a target protein to identify potential drug candidates. These libraries can be virtual, meaning they exist as computer files containing structural information of molecules. PubChem serves as an excellent source for building such virtual libraries. 

Figure 1: PubChem Homepage Interface