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Automated search-model discovery and preparation for structure solution by molecular replacement
Abstract
A novel automation pipeline for macromolecular structure solution by molecular replacement is described. There is a special emphasis on the discovery and preparation of a large number of search models, all of which can be passed to the core molecular-replacement programs. For routine molecular-replacement problems, the pipeline automates what a crystallographer might do and its value is simply one of convenience. For more difficult cases, the pipeline aims to discover the particular template structure and model edits required to produce a viable search model and may succeed in finding an efficacious combination that would be missed otherwise. The pipeline is described in detail and a number of examples are given. The examples are chosen to illustrate successes in real crystallography problems and also particular features of the pipeline. It is concluded that exploring a range of search models automatically can be valuable in many cases.
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Cited by
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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
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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-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
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Graham, W. V., He, W., Marchiando, A. M., Zha, J., Singh, G., Li, H.-S., Biswas, A., Ong, M. L. D. M., Jiang, Z.-H., Choi, W., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0393-7 · Cited by 176
Metadata
- Authors
- Keegan, R. M., & Winn, M. D.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2007-03-16
- Volume
- 63
- Issue
- 4
- Pages
- 447-457
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2070199183
- Cited by
- 160
- References
- 0
- FWCI
- 5.48
- Type
- journal article
- Language
- en
- Open access
- closed
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- Keegan, R. M., & Winn, M. D. (2007). Automated search-model discovery and preparation for structure solution by molecular replacement. Acta Crystallographica Section D Biological Crystallography. https://doi.org/10.1107/s0907444907002661
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