Chemoinformatics is a scientific discipline at the interface between chemistry and computer science, which nowadays is currently implemented in pharmaceutical companies as a part of the usual drug discovery pathway. Furthermore, taking into account the vast amount of experimental and computational data currently generated on drug discovery projects, the use of chemoinformatics tools has become increasingly necessary. Most of chemoinformatics projects are initiated from information stored in large databases of chemicals. The compounds are systematically characterized by numerical descriptors in order to manage this information and obtain some kind of chemical-biological relationships by similarity/diversity analysis, QSAR development for ADMET predictions, chemical space navigation for the selection of drug subspaces, drug-like and lead-like selection, or substructure searching. In this paper, we will review some of the more important chemical databases of small molecules and the descriptors that can be used to describe them, as well as their applications to the specific area of design of focused/targeted libraries.