Active Site Identification

Active site identification defines the specific three-dimensional region of the target protein within which docking calculations will be performed, most...

Active site identification defines the specific three-dimensional region of the target protein within which docking calculations will be performed, most reliably established from the location of a co-crystallised ligand or substrate in an experimental structure. Where no bound ligand is available, computational binding-site prediction algorithms identify candidate pockets on the basis of surface geometry (searching for concave, enclosed cavities of appropriate volume) or evolutionary conservation (favouring pockets lined by residues conserved across orthologous proteins, consistent with functional importance), and the identified site is subsequently validated against any available site-directed mutagenesis or pharmacological data implicating specific residues in ligand or substrate binding.