PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Structural biology, homology modelling and rational drug design require accurate three‐dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re‐refinement of existing structure models in the PDB. A large‐scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X‐ray data as well as in terms of geometric quality. The re‐refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.