PDB_REDO: constructive validation, more than just looking for errors
By Robbie P. Joosten, Krista Joosten, G. Murshudov, Anastassis Perrakis. 2012
197 citations recorded by the source corpus.
The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- T. Croll
- Robbie P. Joosten
- Anastassis Perrakis
- G. Murshudov
- F. Long
- G. Vriend
- Elmar Krieger
- Tim A. H. te Beek
In Molecular Biology
- T. Croll
- Robbie P. Joosten
- Anastassis Perrakis
- G. Murshudov
- F. Long
- G. Vriend
- Elmar Krieger
- Tim A. H. te Beek
Citations in the corpus
- ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, background): “While it often yields impressive improvements in, for example, the Ramachandran plot, particularly for models in the 2–3.3 Å resolution range, beyond about 2.5 Å resolution the typical quality of the final model remains well below that expected at higher resolutions (Joosten et al., 2012).”
- A series of PDB-related databanks for everyday needs (2014, methodology): “New developments in the PDB REDO decision-making algorithms were described elsewhere (23).”
- The PDB_REDO server for macromolecular structure model optimization (2014, methodology): “These programs are linked together by a large set of decision-making algorithms which we have discussed in detail previously (Joosten et al., 2012).”
- A public database of macromolecular diffraction experiments. (2016, background): “…of macromolecular structures, the PDB (Protein ISSN 2059-7983 # 2016 International Union of Crystallography Data Bank, 1971) and related projects (Joosten et al., 2009, 2012; Touw et al., 2015), contain not only the atomic coordinates for each published macromolecular structure, but also key…”
- AceDRG: a stereochemical description generator for ligands (2017, unknown): “In general, while testing various ligands we came to the conclusion that there needs to be some initiative similar to PDB_REDO (Joosten et al. , 2012) to reanalyse all ligands in the PDB.”