The modern drug discovery process is steadily becoming more information driven. Structural, physicochemical and ADME-Tox property profiles of reference (successful) ligands, along with structural information of their target proteins, have been extremely useful for early-stage drug discovery. Recently, databases of known biologically active ligands (knowledge bases) have become more focused toward different protein-target classes. The number of new chemoinformatics tools used to analyze structures and properties of successful molecules has also increased enormously. Scientists in this area are exploring new physicochemical properties and appropriate drug sets to understand druglike properties. In this review, the various uses of the ligand knowledge bases in the drug discovery process have been critically reviewed.