The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
Open accessAbstract
Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a φ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free.
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Cites
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-citationKabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
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
Cited by
Liebschner, 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-citationTowards automated crystallographic structure refinement with phenix.refine
Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444912001308 · Cited by 5,511
Self-citationAutomated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S., & DiMaio, F. (2016) · eLife · doi:10.7554/elife.17219 · Cited by 457
Fadini, A., Li, M., McCoy, A. J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A. R., Jovine, L., Terwilliger, T. C., et al. (2026) · Nature Methods · doi:10.1038/s41592-026-03047-4 · Cited by 22
Du, W., Debski-Antoniak, O., Drabek, D., van Haperen, R., van Dortmondt, M., van der Lee, J., Drulyte, I., van Kuppeveld, F. J. M., Grosveld, F., Hurdiss, D. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49693-0 · Cited by 19
Metadata
- Authors
- Headd, J. J., Echols, N., Afonine, P. V., Grosse-Kunstleve, R. W., Chen, V. B., Moriarty, N. W., Richardson, D. C., Richardson, J. S., & Adams, P. D.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2012-03-16
- Volume
- 68
- Issue
- 4
- Pages
- 381-390
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2017393660
- Cited by
- 252
- References
- 4
- FWCI
- 6.08
- Type
- journal article
- Language
- en
- Open access
- hybrid
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