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.

Raed Khashan, Ph.D.,
Khashan Laboratory for Molecular Modeling & Simulation (

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.