The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions
Open accessAbstract
The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps.REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting,ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool,LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.
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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
Self-citationMolProbity : 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
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-citationRELION: Implementation of a Bayesian approach to cryo-EM structure determination
Scheres, S. H. W. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.09.006 · Cited by 5,446
Rosenthal, P. B., & Henderson, R. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.07.013 · Cited by 2,416
Kühlbrandt, W. (2014) · Science · doi:10.1126/science.1251652 · Cited by 1,325
Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.008 · Cited by 295
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Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586
Real-space refinement in PHENIX for cryo-EM and crystallography
Afonine, P. V., Poon, B. K., Read, R. J., Sobolev, O. V., Terwilliger, T. C., Urzhumtsev, A., & Adams, P. D. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318006551 · Cited by 3,281
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody
Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2349-y · Cited by 1,885
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Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · doi:10.1101/2020.04.07.023903 · Cited by 1,752
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
Barad, B. A., Echols, N., Wang, R. Y.-R., Cheng, Y., DiMaio, F., Adams, P. D., & Fraser, J. S. (2015) · Nature Methods · doi:10.1038/nmeth.3541 · Cited by 886
Metadata
- Authors
- Brown, A., Long, F., Nicholls, R. A., Toots, J., Emsley, P., & Murshudov, G.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2015-01-01
- Volume
- 71
- Issue
- 1
- Pages
- 136-153
- ISSN
- 0907-4449 (ISSN-L)
- 1399-0047
- OpenAlex
- W2097604487
- Cited by
- 618
- References
- 7
- FWCI
- 26.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Brown, A., Long, F., Nicholls, R. A., Toots, J., Emsley, P., & Murshudov, G. (2015). Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallographica Section D Biological Crystallography. https://doi.org/10.1107/s1399004714021683
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