Chemistry

Chemistry & Drug Discovery

Overview

Computational chemistry, cheminformatics, and drug discovery workflows.

Key Tools

• RDKit: Molecular manipulation, fingerprints, descriptors, substructure search
• PubChem: Chemical compound database (100M+ compounds)
• ChEMBL: Bioactivity database for drug-like molecules
• Open Babel: Format conversion, 3D generation
• AutoDock Vina: Molecular docking
• GROMACS/OpenMM: Molecular dynamics simulations

Common Workflows

Virtual Screening

1. Define target (protein structure from PDB)
2. Prepare compound library (from ChEMBL/ZINC/Enamine)
3. Filter by drug-likeness (Lipinski's Rule of Five)