Small Molecule Databases
Small molecule databases play a critical role in bioinformatics, medicinal chemistry, and drug discovery by providing comprehensive information about chemical compounds. Here are some key small molecule databases:
1. PubChem
PubChem is a free, open-access database maintained by the National Center for Biotechnology Information (NCBI). It provides information on the biological activities of small molecules.
Contains data on chemical structures, bioactivity, toxicity, and molecular properties. It is widely used for drug discovery and chemical biology research.
Applications:
Researchers use PubChem to explore the relationship between chemical structures and their biological activities, enabling drug design, bioactivity analysis, and virtual screening.
2. DrugBank
DrugBank is a comprehensive resource combining detailed drug data with drug target information. It is widely used in drug discovery and pharmacology.
Includes information on drugs, their mechanisms of action, interactions, pharmacokinetics, and clinical trials. Both FDA-approved and experimental drugs are cataloged.
Applications:
This database is invaluable for pharmacologists, chemists, and clinicians for drug repurposing, interaction studies, and understanding drug metabolism.
3. ZINC
ZINC is a free database of commercially available chemical compounds provided by the University of California, San Francisco.
Contains over 230 million purchasable compounds in ready-to-dock, 3D formats. ZINC is primarily used in virtual screening for drug discovery.
Applications:
Used for docking simulations, where researchers test the binding affinity of small molecules to target proteins in silico.
4. Cambridge Structural Database (CSD)
The Cambridge Structural Database (CSD) is a curated repository of crystal structures of small organic and metal-organic molecules.
Contains over one million crystal structures, providing insights into molecular geometries, bonding, and interactions. It includes data on molecular conformation, packing, and other structural parameters.
Applications:
Researchers use CSD to study the structure-function relationships of molecules, especially in crystallography and materials science.
