title: PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
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.
authors.forename: Robbie P
authors.initials: RP
authors.lastname: Joosten
authors.forename: Jean
authors.initials: J
authors.lastname: Salzemann
authors.forename: Vincent
authors.initials: V
authors.lastname: Bloch
authors.forename: Heinz
authors.initials: H
authors.lastname: Stockinger
authors.forename: Ann-Charlott
authors.initials: AC
authors.lastname: Berglund
authors.forename: Christophe
authors.initials: C
authors.lastname: Blanchet
authors.forename: Erik
authors.initials: E
authors.lastname: Bongcam-Rudloff
authors.forename: Christophe
authors.initials: C
authors.lastname: Combet
authors.forename: Ana L
authors.initials: AL
authors.lastname: Da Costa
authors.forename: Gilbert
authors.initials: G
authors.lastname: Deleage
authors.forename: Matteo
authors.initials: M
authors.lastname: Diarena
authors.forename: Roberto
authors.initials: R
authors.lastname: Fabbretti
authors.forename: Géraldine
authors.initials: G
authors.lastname: Fettahi
authors.forename: Volker
authors.initials: V
authors.lastname: Flegel
authors.forename: Andreas
authors.initials: A
authors.lastname: Gisel
authors.forename: Vinod
authors.initials: V
authors.lastname: Kasam
authors.forename: Timo
authors.initials: T
authors.lastname: Kervinen
authors.forename: Eija
authors.initials: E
authors.lastname: Korpelainen
authors.forename: Kimmo
authors.initials: K
authors.lastname: Mattila
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.forename: Matthieu
authors.initials: M
authors.lastname: Reichstadt
authors.forename: Vincent
authors.initials: V
authors.lastname: Breton
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Tickle
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend