Protein Structure Retrieval (PDB)

The first practical step of any structure-based design or docking exercise is retrieval of an appropriate three-dimensional target structure, most commonly...

The first practical step of any structure-based design or docking exercise is retrieval of an appropriate three-dimensional target structure, most commonly obtained from the Protein Data Bank (PDB), the internationally curated public repository of experimentally determined macromolecular structures. Structure selection requires careful evaluation of resolution (with structures below approximately 2.5 Å generally considered suitable for docking studies), the presence of a co-crystallised ligand occupying the binding site of interest (which both confirms the biologically relevant site and provides a valuable positive-control pose for docking validation), and the completeness of the modelled structure, since crystallographic structures frequently contain unresolved loop regions that must be addressed during subsequent protein preparation. Where no experimental structure is available for a target of interest, homology modelling — constructing a three-dimensional model based on a related protein of known structure — or, increasingly, deep-learning-based structure prediction tools such as AlphaFold, provide viable alternative sources of a starting structural model.