As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand’s fragment(s) corresponding to that binding pocket are extracted, thus, forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.


The program is an Open Source software that is available at no charge. It is supplied as is, without warranty, and may be freely used and distributed under the terms of the Gnu General Public License (GPL).
To download the program, which runs under Linux, follow this link: FragVLib_to_public.tar.gz


Khashan, R. (2012) FragVLib a free database mining software for generating “Fragment-based Virtual Library” using pocket similarity search of ligand-receptor complexes. J Cheminform 4, 18.