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

Raed Khashan

doi:10.1186/1758-2946-4-18

Abstract

BackgroundWith 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.ResultsThe 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.ConclusionsAn 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.

Highlights

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
Due to the exponential increase of available ligandreceptor complexes, an increasing interest is dedicated to the development of computational tools for mining useful information which can facilitate the drug design and development process [1,2,3,4]
We present a tool that mine database(s) of ligand-receptor complexes and generate a library of fragments for a target receptor so it can be used for structure-based drug design, such as Fragment-Based Lead Discovery (FBLD)

Summary

Results

The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. The ligand's fragment(s) corresponding to that binding pocket are extracted, forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design

Conclusions

Background

Discussion

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