The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
PDB_REDO: constructive validation, more than just looking for errors
Open accessAbstract
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.
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Cites
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581
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MolProbity : all-atom structure validation for macromolecular crystallography
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Overview of the CCP 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353
Self-citationAnnouncing the worldwide Protein Data Bank
Berman, H., Henrick, K., & Nakamura, H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1203-980 · Cited by 3,093
A real-space refinement procedure for proteins
Diamond, R. (1971) · Acta Crystallographica Section A · doi:10.1107/s0567739471000986 · Cited by 236
Flück, C. E., Pandey, A. V., Dick, B., Camats, N., Fernández-Cancio, M., Clemente, M., Gussinyé, M., Carrascosa, A., Mullis, P. E., & Audi, L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020178 · Cited by 94
Cited by
Croll, T. I. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318002425 · Cited by 2,038
A series of PDB related databases for everyday needs
Joosten, R. P., te Beek, T. A. H., Krieger, E., Hekkelman, M. L., Hooft, R. W. W., Schneider, R., Sander, C., & Vriend, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1105 · Cited by 1,293
Self-citationA series of PDB-related databanks for everyday needs
Touw, W. G., Baakman, C., Black, J., te Beek, T. A. H., Krieger, E., Joosten, R. P., & Vriend, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1028 · Cited by 935
Self-citationThe CCP 4 suite: integrative software for macromolecular crystallography
Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Baslé, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Mármol, J. J., Berrisford, J. M., et al. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323003595 · Cited by 909
Self-citationThe PDB_REDO server for macromolecular structure model optimization
Joosten, R. P., Long, F., Murshudov, G. N., & Perrakis, A. (2014) · IUCrJ · doi:10.1107/s2052252514009324 · Cited by 834
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Metadata
- Authors
- Joosten, R. P., Joosten, K., Murshudov, G. N., & Perrakis, A.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2012-03-16
- Volume
- 68
- Issue
- 4
- Pages
- 484-496
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2154994578
- Cited by
- 213
- References
- 7
- FWCI
- 10.14
- Type
- journal article
- Language
- en
- Open access
- hybrid
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