The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
Open accessAbstract
Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol wizard carries out automated structure solution based on any combination of SAD, MAD, SIR or MIR data sets. The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing.
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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
PHENIX : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361
Self-citationKabsch, W. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889893005588 · Cited by 3,578
Automated protein model building combined with iterative structure refinement.
Anastassis Perrakis, A., Morris, R. J., & Lamzin, V. S. (1999) · Nature Structural Biology · doi:10.1038/8263 · Cited by 2,431
Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution
Sutton, R. B., Fasshauer, D., Jahn, R., & Brunger, A. T. (1998) · Nature · doi:10.1038/26412 · Cited by 2,417
Maximum-likelihood density modification
Terwilliger, T. C. (2000) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444900005072 · Cited by 1,634
Self-citationSubstructure solution with SHELXD
Schneider, T. R., & Sheldrick, G. M. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902011678 · Cited by 1,588
Terwilliger, 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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PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Self-citationLiebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011471 · Cited by 7,953
Self-citationThe Phenix software for automated determination of macromolecular structures
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Echols, N., Headd, J. J., Hung, L.-W., Jain, S., Kapral, G. J., Grosse Kunstleve, R. W., et al. (2011) · Methods · doi:10.1016/j.ymeth.2011.07.005 · Cited by 891
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
Structure of the human glucagon class B G-protein-coupled receptor
Siu, F. Y., He, M., de Graaf, C., Han, G. W., Yang, D., Zhang, Z., Zhou, C., Xu, Q., Wacker, D., Joseph, J. S., et al. (2013) · Nature · doi:10.1038/nature12393 · Cited by 379
Metadata
- Authors
- Terwilliger, T. C., Adams, P. D., Read, R. J., McCoy, A. J., Moriarty, N. W., Grosse-Kunstleve, R. W., Afonine, P. V., Zwart, P. H., & Hung, L.-W.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2009-05-15
- Volume
- 65
- Issue
- 6
- Pages
- 582-601
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2103714813
- Cited by
- 848
- References
- 64
- FWCI
- 6.22
- Type
- journal article
- Language
- en
- Open access
- hybrid
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