PDB REDO
From Proteopedia
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== PDB_REDO == | == PDB_REDO == | ||
| + | A databank with updated and optimised macromolecular X-ray diffraction structure models. [http://www.cmbi.ru.nl/pdb_redo/ http://www.cmbi.ru.nl/pdb_redo/ ] | ||
[[Image:PDB REDO.png|right]] | [[Image:PDB REDO.png|right]] | ||
| + | === Why to ''redo'' PDB? === | ||
| + | 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. | ||
''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 | ''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 | ||
Revision as of 16:01, 1 July 2010
PDB_REDO
A databank with updated and optimised macromolecular X-ray diffraction structure models. http://www.cmbi.ru.nl/pdb_redo/
Why to redo PDB?
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.
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
