The DOI matches its Crossref record.
Likelihood-enhanced fast rotation functions
Abstract
Experiences with the molecular-replacement program Beast have shown that maximum-likelihood rotation targets are more sensitive to the correct orientation than traditional targets. However, this comes at a high computational cost: brute-force rotation searches can take hours or even days of computation time on current desktop computers. Series approximations to the full likelihood target have been developed that can be computed by fast Fourier transforms in minutes. These likelihood-enhanced targets are more sensitive to the correct orientation than the Crowther fast rotation function and they take advantage of information from partial solutions. The likelihood-enhanced rotation targets have been implemented in the program Phaser.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
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-citationPhaser 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-citationDuda, D. M., Borg, L. A., Scott, D. C., Hunt, H. W., Hammel, M., & Schulman, B. A. (2008) · Cell · doi:10.1016/j.cell.2008.07.022 · Cited by 767
Cooperative binding of two acetylation marks on a histone tail by a single bromodomain
Morinière, J., Rousseaux, S., Steuerwald, U., Soler-López, M., Curtet, S., Vitte, A.-L., Govin, J., Gaucher, J., Sadoul, K., Hart, D. J., et al. (2009) · Nature · doi:10.1038/nature08397 · Cited by 469
Structure of a complex of the ATPase SecA and the protein-translocation channel.
Zimmer, J., Nam, Y., & Rapoport, T. A. (2008) · Nature · doi:10.1038/nature07335 · Cited by 459
The Molecular Basis of Filamin Binding to Integrins and Competition with Talin
Kiema, T., Lad, Y., Jiang, P., Oxley, C. L., Baldassarre, M., Wegener, K. L., Campbell, I. D., Ylänne, J., & Calderwood, D. A. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.01.011 · Cited by 434
The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer
Stewart, M. L., Fire, E., Keating, A. E., & Walensky, L. D. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.391 · Cited by 418
Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX
Pazgier, M., Liu, M., Zou, G., Yuan, W., Li, C., Li, C., Li, J., Monbo, J., Zella, D., Tarasov, S. G., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900947106 · Cited by 391
Horton, J. R., Upadhyay, A. K., Qi, H. H., Zhang, X., Shi, Y., & Cheng, X. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1753 · Cited by 389
Molecular basis for LDL receptor recognition by PCSK9
Kwon, H. J., Lagace, T. A., McNutt, M. C., Horton, J. D., & Deisenhofer, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712064105 · Cited by 389
BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer
Dou, H., Buetow, L., Sibbet, G. J., Cameron, K., & Huang, D. T. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2379 · Cited by 319
Fritz, T. A., Raman, J., & Tabak, L. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m513590200 · Cited by 163
Johansson, C., Kavanagh, K. L., Gileadi, O., & Oppermann, U. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m608179200 · Cited by 147
Pogenberg, V., Ögmundsdóttir, M. H., Bergsteinsdóttir, K., Schepsky, A., Phung, B., Deineko, V., Milewski, M., Steingrímsson, E., & Wilmanns, M. (2012) · Genes & Development · doi:10.1101/gad.198192.112 · Cited by 137
Structural basis for recognition of H3K56-acetylated histone H3–H4 by the chaperone Rtt106
Su, D., Hu, Q., Li, Q., Thompson, J. R., Cui, G., Fazly, A., Davies, B. A., Botuyan, M. V., Zhang, Z., & Mer, G. (2012) · Nature · doi:10.1038/nature10861 · Cited by 128
Structure of ERK2 bound to PEA-15 reveals a mechanism for rapid release of activated MAPK
Mace, P. D., Wallez, Y., Egger, M. F., Dobaczewska, M. K., Robinson, H., Pasquale, E. B., & Riedl, S. J. (2013) · Nature Communications · doi:10.1038/ncomms2687 · Cited by 97
Zhao, J., Du, Y., Horton, J. R., Upadhyay, A. K., Lou, B., Bai, Y., Zhang, X., Du, L., Li, M., Wang, B., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100012108 · Cited by 105
Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol
Goedken, E. R., Argiriadi, M. A., Banach, D. L., Fiamengo, B. A., Foley, S. E., Frank, K. E., George, J. S., Harris, C. M., Hobson, A. D., Ihle, D. C., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.595181 · Cited by 101
Kulkarni, K., Yang, J., Zhang, Z., & Barford, D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.236455 · Cited by 97
Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma
Choi, S., Connelly, S., Reixach, N., Wilson, I. A., & Kelly, J. W. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.281 · Cited by 90
Quancard, J., Klein, T., Fung, S.-Y., Renatus, M., Hughes, N., Israël, L., Priatel, J. J., Kang, S., Blank, M. A., Viner, R. I., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-018-0222-1 · Cited by 72
Cheng, X., Wang, Y., Gong, Y., Li, F., Guo, Y., Hu, S., Liu, J., & Pan, L. (2016) · Autophagy · doi:10.1080/15548627.2016.1185590 · Cited by 62
Zhao, B., Moody, S. C., Hider, R. C., Lei, L., Kelly, S. L., Waterman, M. R., & Lamb, D. C. (2012) · International Journal of Molecular Sciences · doi:10.3390/ijms13078500 · Cited by 42
Leonarski, F., D'Ascenzo, L., & Auffinger, P. (2019) · RNA · doi:10.1261/rna.068437.118 · Cited by 39
Ma, W., Shang, Y., Wei, Z., Wen, W., Wang, W., & Zhang, M. (2010) · Structure · doi:10.1016/j.str.2010.08.011 · Cited by 31
Caria, S., Magtoto, C. M., Samiei, T., Portela, M., Lim, K. Y. B., How, J. Y., Stewart, B. Z., Humbert, P. O., Richardson, H. E., & Kvansakul, M. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.817528 · Cited by 28
Likelihood-based docking of models into cryo-EM maps
Millán, C., McCoy, A. J., Terwilliger, T. C., & Read, R. J. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323001602 · Cited by 23
Self-citationCrystal structure of the human Scribble PDZ 1 domain bound to the PDZ ‐binding motif of APC
How, J. Y., Caria, S., Humbert, P. O., & Kvansakul, M. (2019) · FEBS Letters · doi:10.1002/1873-3468.13329 · Cited by 19
Pathuri, P., Nguyen, E. T., Ozorowski, G., Svärd, S. G., & Luecke, H. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.11.012 · Cited by 19
Pathuri, P., Nguyen, E. T., Svärd, S. G., & Luecke, H. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.02.016 · Cited by 18
Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity
Zhou, X., Zhang, H., Wang, Y., Wang, D., Lin, Z., Zhang, Y., Tang, Y., Liu, J., Yao, Y.-F., Zhang, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58432-y · Cited by 17
Crystal Structure of Human ASB9-2 and Substrate-Recognition of CKB
Fei, X., Gu, X., Fan, S., Yang, Z., Li, F., Zhang, C., Gong, W., Mao, Y., & Ji, C. (2012) · The Protein Journal · doi:10.1007/s10930-012-9401-1 · Cited by 12
Structural basis of calcium-dependent C1ql1/BAI3 assemblies in synaptic connectivity
Liao, L., Han, Y., Niu, F., Wang, Y., Lu, Y., Xu, S., Zhu, H., Lin, L., Xiao, J., Tou, H. I., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-66254-1 · Cited by 4
Metadata
- Authors
- Storoni, L. C., McCoy, A. J., & Read, R. J.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2004-02-25
- Volume
- 60
- Issue
- 3
- Pages
- 432-438
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2016765195
- Cited by
- 1,172
- References
- 0
- FWCI
- 71.86
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
