Provide examples of common molecular databases used in chemoinformatics and their specific focus areas.
Several molecular databases are widely used in chemoinformatics, each with its specific focus areas and applications. Here are some common examples:
1. PubChem:
- Focus Area: General Chemical Information
- Description: PubChem, maintained by the National Center for Biotechnology Information (NCBI), is a comprehensive database of chemical compounds. It includes information on chemical structures, biological activities, and references to scientific literature. PubChem serves as a valuable resource for chemoinformatics, supporting diverse applications in drug discovery, toxicity prediction, and chemical biology.
2. ChEMBL:
- Focus Area: Bioactivity Data
- Description: ChEMBL is a bioactivity database that provides information on the binding properties of small molecules to their intended biological targets. It includes data on compounds tested in various assays, their potencies, and target information. ChEMBL is widely used in chemoinformatics for drug discovery and the development of quantitative structure-activity relationship (QSAR) models.
3. ChemSpider:
- Focus Area: Chemical Structure Database
- Description: ChemSpider, provided by the Royal Society of Chemistry, is a chemical structure database that aggregates information on millions of chemical compounds. It includes data on chemical names, structures, properties, and links to external resources. ChemSpider is valuable for searching and retrieving chemical information in diverse research areas.
4. ZINC:
- Focus Area: Drug-Like Compounds
- Description: ZINC is a database of commercially available chemical compounds focused on drug discovery. It provides a curated collection of virtual screening libraries, allowing researchers to access a diverse set of drug-like compounds for virtual screening and ligand-based design.
5. DrugBank:
- Focus Area: Drug Information
- Description: DrugBank is a comprehensive database that integrates information on drugs, drug targets, and drug mechanisms of action. It includes details on FDA-approved drugs, experimental drugs, and their respective targets. DrugBank supports chemoinformatics applications in drug repurposing, target identification, and pharmacological profiling.
6. BindingDB:
- Focus Area: Protein-Ligand Binding Data
- Description: BindingDB is a database that focuses on experimentally determined protein-ligand binding data. It provides information on binding affinities and thermodynamics for a wide range of protein-ligand complexes. BindingDB is valuable for researchers involved in structure-based drug design and ligand-protein interaction studies.
7. ChemBank:
- Focus Area: Small Molecule Screening Data
- Description: ChemBank is a database that primarily focuses on small molecule screening data from high-throughput experiments. It includes information on bioassays, screening results, and chemical structures. ChemBank supports chemoinformatics research related to compound screening, hit identification, and chemical genomics.
8. PDB (Protein Data Bank):
- Focus Area: Protein Structures
- Description: While not exclusively a chemical database, the PDB is a repository of experimentally determined 3D structures of biological macromolecules, including proteins and nucleic acids. It is a valuable resource for researchers in chemoinformatics who need structural information for ligand docking studies and structure-based drug design.
These databases provide a foundation for various chemoinformatics applications, ranging from compound screening and structure-activity relationship analysis to the exploration of protein-ligand interactions and drug repurposing efforts. Researchers often integrate data from multiple databases to gain a comprehensive understanding of chemical and biological information.