The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Recent developments in the CCP-EM software suite
Open accessAbstract
As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.
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
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
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
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-citationBiopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012) · Nature Methods · doi:10.1038/nmeth.1818 · Cited by 2,288
Kühlbrandt, W. (2014) · Science · doi:10.1126/science.1251652 · Cited by 1,325
Cited by
Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex
Lawrence, R. E., Fromm, S. A., Fu, Y., Yokom, A. L., Kim, D. J., Thelen, A. M., Young, L. N., Lim, C.-Y., Samelson, A. J., Hurley, J. H., et al. (2019) · Science · doi:10.1126/science.aax0364 · Cited by 192
In situ single particle classification reveals distinct 60S maturation intermediates in cells
Lucas, B. A., Zhang, K., Loerch, S., & Grigorieff, N. (2022) · eLife · doi:10.7554/elife.79272 · Cited by 53
Kouba, T., Vogel, D., Thorkelsson, S. R., Quemin, E. R. J., Williams, H. M., Milewski, M., Busch, C., Günther, S., Grünewald, K., Rosenthal, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27305-5 · Cited by 50
von Kügelgen, A., van Dorst, S., Yamashita, K., Sexton, D. L., Tocheva, E. I., Murshudov, G., Alva, V., & Bharat, T. A. M. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215808120 · Cited by 35
Structural basis of the mechanism and inhibition of a human ceramide synthase
Pascoa, T. C., Pike, A. C. W., Tautermann, C. S., Chi, G., Traub, M., Quigley, A., Chalk, R., Štefanić, S., Thamm, S., Pautsch, A., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01414-3 · Cited by 25
Giri, N., Wang, L., & Cheng, J. (2024) · Scientific Data · doi:10.1038/s41597-024-03299-9 · Cited by 17
Calcraft, T., Stanke-Scheffler, N., Nans, A., Lindemann, D., Taylor, I. A., & Rosenthal, P. B. (2024) · Cell · doi:10.1016/j.cell.2024.06.017 · Cited by 14
Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase
Bulvas, O., Knejzlík, Z., Sýs, J., Filimoněnko, A., Čížková, M., Clarová, K., Rejman, D., Kouba, T., & Pichová, I. (2024) · Nature Communications · doi:10.1038/s41467-024-50933-6 · Cited by 13
Using deep-learning predictions of inter-residue distances for model validation
Sánchez Rodríguez, F., Chojnowski, G., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322010415 · Cited by 11
Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface
Lethier, M., Huard, K., Hons, M., Favier, A., Brutscher, B., Boeri Erba, E., Abbott, D. W., Cusack, S., & Pellegrini, E. (2023) · Life Science Alliance · doi:10.26508/lsa.202201784 · Cited by 11
Structural journey of an insecticidal protein against western corn rootworm
Marini, G., Poland, B., Leininger, C., Lukoyanova, N., Spielbauer, D., Barry, J. K., Altier, D., Lum, A., Scolaro, E., Ortega, C. P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39891-7 · Cited by 9
Bimai, O., Banerjee, I., Rozman Grinberg, I., Huang, P., Hultgren, L., Ekström, S., Lundin, D., Sjöberg, B.-M., & Logan, D. T. (2024) · eLife · doi:10.7554/elife.89292 · Cited by 3
Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
Read, R. J., Pettersen, E. F., McCoy, A. J., Croll, T. I., Terwilliger, T. C., Poon, B. K., Meng, E. C., Liebschner, D., & Adams, P. D. (2024) · doi:10.1101/2024.05.16.594509 · Cited by 1
Bimaï, O., Banerjee, I., Grinberg, I. R., Huang, P., Hultgren, L., Ekström, S., Lundin, D., Sjöberg, B.-M., & Logan, D. T. (2023) · doi:10.1101/2023.06.20.545753 · Cited by 1
Insights from aquaporin structures into drug-resistant sleeping sickness
Matusevicius, M., Corey, R. A., Gragera, M., Yamashita, K., Sprenger, T., Ungogo, M. A., Blaza, J. N., Castro-Hartmann, P., Chirgadze, D. Y., Chaitanya Vedithi, S., et al. (2025) · doi:10.1101/2025.05.15.654314 · Cited by 1
Metadata
- Authors
- Burnley, T., Palmer, C. M., & Winn, M.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2017-05-31
- Volume
- 73
- Issue
- 6
- Pages
- 469-477
- ISSN
- 2059-7983 (ISSN-L)
- OpenAlex
- W2620712420
- Cited by
- 355
- References
- 6
- FWCI
- 9.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
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.