The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
The PDB_REDO server for macromolecular structure model optimization
Open accessAbstract
The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al.(2011),Structure,19, 1395–1412]. The PDB_REDO procedure aims for `constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallographers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure,e.g.testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria,e.g.the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.
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Cites
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
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-citationLinking Crystallographic Model and Data Quality
Karplus, P. A., & Diederichs, K. (2012) · Science · doi:10.1126/science.1218231 · Cited by 1,781
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728 · cited 2×
“Additional validation is performed by pdb-care for carbohydrates (Lütteke & von der Lieth, 2004) and FoldX (Guerois et al., 2002) for calculation of the Gibbs folding energy.”
MethodTerwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J., & Adams, P. D. (2008) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490705024x · Cited by 1,462
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Design of protein-binding proteins from the target structure alone
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Cerutti, G., Guo, Y., Zhou, T., Gorman, J., Lee, M., Rapp, M., Reddem, E. R., Yu, J., Bahna, F., Bimela, J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.005 · Cited by 519
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Structural basis of BRCC36 function in DNA repair and immune regulation
Rabl, J., Bunker, R. D., Schenk, A. D., Cavadini, S., Gill, M. E., Abdulrahman, W., Andrés-Pons, A., Luijsterburg, M. S., Ibrahim, A. F. M., Branigan, E., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.002 · Cited by 84
Metadata
- Authors
- Joosten, R. P., Long, F., Murshudov, G. N., & Perrakis, A.
- Venue
- IUCrJ
- Published
- 2014-05-30
- Volume
- 1
- Issue
- 4
- Pages
- 213-220
- ISSN
- 2052-2525 (ISSN-L)
- OpenAlex
- W2131417105
- Cited by
- 834
- References
- 6
- FWCI
- 25.02
- Type
- journal article
- Language
- en
- Open access
- gold
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