Computational methods based on molecular shape
Elisabet Gregori‐Puigjané · 2013
The comparison of chemical entities has been, and still is, one of the main ways to link biology and chemistry. Whether it is used to compare small molecules and infer the pharmacological profile of a query compound, to study the complementarity of chemical entities through small-molecule or protein–protein docking, or to predict a protein’s function through similarity of its binding site to proteins with known function, the mathematical description of these chemical entities is a crucial step. Here, this chapter will discuss how incorporating shape, together with pharmacophoric feature comparison, presents unique possibilities and advantages. The current state of the art methods in this field and the caveats and limitations of shape-based methods will also be discussed.