View source for PDB REDO

== PDB_REDO ==
A databank with updated and optimised macromolecular X-ray diffraction structure models. [https://pdb-redo.eu/ pdb-redo.eu]
[[Image:PDB REDO.png|right]]
=== 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 [https://pdb-redo.eu/ pdb-redo.eu].
# Enter the [[PDB ID]] of a published structure.
# Download the re-refined and rebuilt PDB file.
# [http://firstglance.jmol.org/where.htm#uploading Upload] it to [http://firstglance.jmol.org FirstGlance in Jmol] or open it in [[Molecular modeling and visualization software|another viewer]].