CHAPTER 4: Molecular Similarity

The concept of molecular similarity is key in many aspects of medicinal chemistry, from structural clustering to identify groups of chemical structures that are likely to exhibit similar properties, to molecular diversity methods to discover subsets of structures that cover the extent of the molecular diversity represented in a given data set. This chapter lays out the concept of molecular similarity, including challenges in the underlying subjectivity of the concept and approaches to provide more objective measures of molecular similarity. The advantages and potential limitations will be discussed and advice given on how one might appropriately apply these methods in drug discovery.