Molecular Databases

Compound databases (DBs) aim to organize the information needed for the initial stages of drug discovery. The collection and organization of curated information from bibliographic searches in DBs helps the scientific community to develop multidisciplinary research areas. For example, the chemical and biological properties contained in compound libraries, including PubChem, ZINC, BindingDB, and ChEMBL, are widely used in drug discovery projects. The importance of DBs in these projects is continuously increasing, beyond their role as compound repositories. In fact, compound DBs and chemical datasets can be a centerpiece in pharmaceutical companies, as well as in academic and government research centers. Several research groups have recently used computational methodologies to screen large DBs of compounds before experimental screening and designing their experiments. The number of DB compounds in the public domain, including those for compounds of natural origin, is increasing. This is in line with the growing and synergistic combination of natural product research and chemoinformatics, for example, NuBBEDB (Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products) and BIOFACQUIM (A Mexican Compound Database of Natural Products). Developing a database involves four steps. Step 1—Search for chemical or biological information in indexed databases that report the strategies used to find the information that will make up the DBs. Step 2—Curation: describes the database (DB) curation processes, automated or manual. Step 3—DB management and network visualization: describes different systems to process DBs. Step 4—Update and maintenance: The last and most important stage is that, in addition to the development of a DB, its maintenance requires various resources, both financial and human. The quality of the compound DBs is crucial to fulfill properly their role as drug design tools. For automated curation, some tools can be used, such as KNIME and Open Babel. Currently, and in the near future, these virtual libraries could also enrich the medically relevant chemical space for inhibitors and potential drug candidates. In addition, the incorporation of chemoinformatics tools, the automation of curation processes, and the allocation of financial and human resources for the maintenance of DBs will contribute significantly to the development of drug design discovery and development projects.