PDB_REDO: automated re-refinement of X-ray structure models in the PDB
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Open Access
- 3 April 2009
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Journal of Applied Crystallography
- Vol. 42 (3) , 376-384
- https://doi.org/10.1107/s0021889809008784
Abstract
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.Keywords
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