The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
High-resolution structure prediction and the crystallographic phase problem
Open accessAbstract
The energy-based refinement of low-resolution protein structure models to atomic-level accuracy is a major challenge for computational structural biology. Here we describe a new approach to refining protein structure models that focuses sampling in regions most likely to contain errors while allowing the whole structure to relax in a physically realistic all-atom force field. In applications to models produced using nuclear magnetic resonance data and to comparative models based on distant structural homologues, the method can significantly improve the accuracy of the structures in terms of both the backbone conformations and the placement of core side chains. Furthermore, the resulting models satisfy a particularly stringent test: they provide significantly better solutions to the X-ray crystallographic phase problem in molecular replacement trials. Finally, we show that all-atom refinement can produce de novo protein structure predictions that reach the high accuracy required for molecular replacement without any experimental phase information and in the absence of templates suitable for molecular replacement from the Protein Data Bank. These results suggest that the combination of high-resolution structure prediction with state-of-the-art phasing tools may be unexpectedly powerful in phasing crystallographic data for which molecular replacement is hindered by the absence of sufficiently accurate previous models.
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Cites
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
Self-citationGlover, F., & Laguna, M. (1997) · doi:10.1007/978-1-4615-6089-0 · Cited by 3,001
LGA: a method for finding 3D similarities in protein structures
Zemla, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg571 · Cited by 1,069
Cited by
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
Langer, G., Cohen, S. X., Lamzin, V. S., & Perrakis, A. (2008) · Nature Protocols · doi:10.1038/nprot.2008.91 · Cited by 1,606
Predicting protein structures with a multiplayer online game
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) · Nature · doi:10.1038/nature09304 · Cited by 1,368
Self-citationProtein structure prediction: when is it useful?
Zhang, Y. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.02.005 · Cited by 277
Implications of AlphaFold 2 for crystallographic phasing by molecular replacement
McCoy, A. J., Sammito, M. D., & Read, R. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798321012122 · Cited by 104
Self-citationHe, X., Lobsiger, J., & Stocker, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907454106 · Cited by 73
Integrative structure modeling of macromolecular assemblies from proteomics data
Lasker, K., Phillips, J. L., Russel, D., Velázquez-Muriel, J., Schneidman-Duhovny, D., Tjioe, E., Webb, B., Schlessinger, A., & Sali, A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r110.000067 · Cited by 71
Assessing the utility of CASP14 models for molecular replacement
Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26214 · Cited by 62
Self-citationIntegrative Structural Biology in the Era of Accurate Structure Prediction
Masrati, G., Landau, M., Ben-Tal, N., Lupas, A., Kosloff, M., & Kosinski, J. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167127 · Cited by 53
Barbarin-Bocahu, I., & Graille, M. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322002157 · Cited by 52
Xia, Y., DiPrimio, N., Keppel, T. R., Vo, B., Fraser, K., Battaile, K. P., Egan, C., Bystroff, C., Lovell, S., Weis, D. D., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja407644b · Cited by 33
Evaluation of model refinement in CASP14
Simpkin, A. J., Sánchez Rodríguez, F., Mesdaghi, S., Kryshtafovych, A., & Rigden, D. J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26185 · Cited by 28
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322003576 · Cited by 24
Metadata
- Authors
- Qian, B., Raman, S., Das, R., Bradley, P., McCoy, A. J., Read, R. J., & Baker, D.
- Venue
- Nature
- Published
- 2007-10-14
- Volume
- 450
- Issue
- 7167
- Pages
- 259-264
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2053197719
- Cited by
- 316
- References
- 3
- FWCI
- 11.49
- Type
- journal article
- Language
- en
- Open access
- green
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