PDB REDO
From Proteopedia
PDB_REDO
A databank with updated and optimised macromolecular X-ray diffraction structure models. pdb-redo.eu
Why redo PDB files?
The goal of PDB_REDO is to provide optimised structure models for a wide range of PDB users (biologist, (bio)chemist, drug designers, teachers and the general public) and uniform datasets for method developers in structural biology.
Because the method used to create PDB_REDO entries is fully automated, all structures are treated consistently and objectively. The automation also makes it possible to provide redone structure models shortly after they are released in the PDB.
The PDB_REDO method can improve about two-thirds of the protein structures in the PDB (in terms of R-free) by re-refinement. Further optimisation of structure models by rebuilding side chains and performing 'peptide flips' increases the success rate (a ref will hopefully be here at some point). Of course, rebuilding can change the interpretation of the experimental data substantially, therefore models redone with and without rebuilding are provided. This enables the user to choose between the interpretation of the original depositor and that of PDB_REDO.
PDB_REDO: automated re-refinement of X-ray structure models in the PDB, Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G (2009) JOURNAL OF APPLIED CRYSTALLOGRAPHY 42 : 376-384
How To ReDo
- Go to pdb-redo.eu.
- Enter the PDB ID of a published structure.
- Download the re-refined and rebuilt PDB file.
- Upload it to FirstGlance in Jmol or open it in another viewer.
