text: Given a set of structurally diverse ligands that binds to a receptor, a model of the receptor can be built by exploiting the collective information contained in such set of ligands.  Different computational techniques explore the structural, electronic, molecular shape, and physicochemical similarities of different ligands that could imply their mode of action against a specific molecular receptor or cell lines.  A candidate ligand can then be compared to the pharmacophore model to determine whether it is compatible with it and therefore likely to bind. Different 2D chemical similarity analysis methods have been used to scan a databases to find active ligands. Another popular approach used in ligand-based virtual screening consist on searching molecules with shape similar to that of known actives, as such molecules will fit the target's binding site and hence will be likely to bind the target. There are a number of prospective applications of this class of techniques in the literature. Pharmacophoric extensions of these 3D methods are also freely-available as webservers. Also shape based virtual screening has gained significant popularity.