title: Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.
abstract: 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.
authors.affiliation: Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, 31982, Saudi Arabia, rkhashan@kfu.edu.sa.
authors.forename: Raed S
authors.initials: RS
authors.lastname: Khashan
mesh_terms: D001665:Binding Sites / Q000235:genetics*; D057225:Data Mining / Q000379:methods*; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D057386:Search Engine; D054852:Small Molecule Libraries; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins; D054852:Small Molecule Libraries