A pharmacophore is a model which represents the key physico-chemical 
interactions that mediate biological activity. There is a long history of using 
pharmacophore modeling methods to select subsets of compounds, focused towards a 
specific target of interest. This paper will review existing computational 
methods for deriving and comparing pharmacophore models. We outline a new 
classification of pharmacophore methods based on the abstraction of the 
underlying chemical interactions which embody a pharmacophore, and the methods 
available to quantitatively compare them. Within the context of this 
classification, example studies, using specific pharmacophore modeling methods 
for focused library selection, will be discussed.