Implementing an X-ray validation pipeline for the Protein Data Bank

By Swanand P. Gore, S. Velankar, Gerard J. Kleywegt. 2012

95 citations recorded by the source corpus.

The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described.

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

1. Paul D. Adams
2. Nigel W. Moriarty
3. Jane S. Richardson
4. David C Richardson
5. Torsten Schwede
6. Vincent B. Chen
7. J. Headd
8. Pavel V. Afonine

In Molecular Biology

1. Paul D. Adams
2. Torsten Schwede
3. Nigel W. Moriarty
4. Jane S. Richardson
5. David C Richardson
6. Vincent B. Chen
7. Gabriel Studer
8. B. Hintze

Citations in the corpus

• Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO) (2019, methodology): “Sets of previously established validation criteria will be employed for this task, which are based on the reports of the PDB validation pipeline.(39) We envision to include ligand poses as well as assess heteromers in the near future stimulating the development of structure prediction methods even f”
• MolProbity: More and better reference data for improved all‐atom structure validation (2018, methodology): “They are now used for X-ray crystallography 18,19 and for nuclear magnetic resonance, 20 and may also be adopted for cryo electron microscopy.”
• Model validation: local diagnosis, correction and when to quit (2018, methodology): “All-atom contact analysis, as performed in MolProbity (Chen et al., 2010), PHENIX (Adams et al., 2010), Coot (Emsley et al., 2010) and wwPDB validation (Berman et al., 2003; Read et al., 2011; Gore et al., 2012), first requires REDUCE to be run (Word, Lovell, Richardson et al., 1999).”
• PDBe: improved accessibility of macromolecular structure data from PDB and EMDB (2015, methodology): “As part of the wwPDB collaboration, PDBe has implemented a validation pipeline (41) based on the recommendations of the X-ray Validation Task Force (VTF) (42).”
• The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, methodology): “RCSB PDB provides access to geometric validation and other information, including the Validation Reports for all X-ray structures generated by the wwPDB (55).”