FragVLib a free database mining software for generating "Fragment-based Virtual Library" using pocket similarity search of ligand-receptor complexes

Background With the exponential increase in the number of available ligand-receptor complexes, researchers are becoming more dedicated to mine these complexes to facilitate the drug design and development process. Therefore, we present FragVLib, free software which is developed as a tool for performing similarity search across database(s) of ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. Results 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. Conclusions An efficient algorithm is implemented in FragVLib to facilitate the pocket similarity search. The resulting fragments can be used for structure-based drug design tools such as Fragment-Based Lead Discovery (FBLD). They can also be used for finding bioisosteres and as an idea generator.