Open AccessPDB_REDO : constructive validation, more than just looking for errors
Author(s) -
Joosten Robbie P.,
Joosten Krista,
Murshudov Garib N.,
Perrakis Anastassis
Publication year - 2012
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444911054515
Subject(s) - protein data bank (rcsb pdb) , computer science , pipeline (software) , consistency (knowledge bases) , protein data bank , software , data mining , algorithm , crystallography , programming language , protein structure , artificial intelligence , chemistry , biochemistry , stereochemistry
Developments of the PDB_REDO procedure that combine re‐refinement and rebuilding within a unique decision‐making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom‐built software modules to choose an optimal refinement protocol ( e.g. anisotropic, isotropic or overall B ‐factor refinement, TLS model) and to optimize the geometry versus data‐refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.