LiSiCA

LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format.

The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly.

In 2D and 3D screening the molecular graph vertices represent atoms.

In 2D screening edges of molecular graph represent covalent bonds while in 3D screening edges are drawn between every pair of vertices and have no chemical meaning.

A product graph generated from molecular graphs is then searched using fast maximum clique algorithm[1][2] to find the largest substructure common to both compounds.

An example of 2D screening with LiSiCA PyMOL plugin.
An example of 3D screening with LiSiCA PyMOL plugin.