Recent developments in computer power and chemoinformatics methodology make possible that a huge amount of data become available through internet. These databases are devoted to a wide spectrum of scientific fields. Here we are concerned with databases related to protein-drug interactions. More specifically, databases where potential new molecules could be accessed to be used in virtual screening initiatives. In the past decade several databases have been developed where molecules to be used in the virtual screening could be easily identified, downloaded and even purchased. This review describes and summarizes the recent advances in the development of these databases, and also the main applications related to virtual screening projects.