The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
Open accessAbstract
One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.
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
(1999) · Choice Reviews Online · doi:10.5860/choice.37-0940 · Cited by 14,314
A real-space refinement procedure for proteins
Diamond, R. (1971) · Acta Crystallographica Section A · doi:10.1107/s0567739471000986 · Cited by 236
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
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-citationLiebschner, 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
Towards 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
MolProbity: More and better reference data for improved all‐atom structure validation
Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., et al. (2018) · Protein Science · doi:10.1002/pro.3330 · Cited by 4,599
Non-Homeostatic Body Weight Regulation Through a Brainstem-Restricted Receptor for GDF15
Hsu, J.-Y., Crawley, S., Chen, M., Ayupova, D. A., Lindhout, D. A., Higbee, J., Kutach, A., Joo, W., Gao, Z., Fu, D., et al. (2017) · Nature · doi:10.1038/nature24042 · Cited by 616
Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion
Walls, A. C., Xiong, X., Park, Y.-J., Tortorici, M. A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.028 · Cited by 582
The role of protein dynamics in the evolution of new enzyme function
Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2175 · Cited by 311
Bian, C., Xu, C., Ruan, J., Lee, K. K., Burke, T. L., Tempel, W., Barsyte, D., Li, J., Wu, M., Zhou, B. O., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.193 · Cited by 281
Ward, R. A., Anderton, M. J., Ashton, S., Bethel, P. A., Box, M., Butterworth, S., Colclough, N., Chorley, C. G., Chuaqui, C., Cross, D. A. E., et al. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm400822z · Cited by 279
Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators
Song, G., Yang, D., Wang, Y., de Graaf, C., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., et al. (2017) · Nature · doi:10.1038/nature22378 · Cited by 241
Hepcidin Revisited, Disulfide Connectivity, Dynamics, and Structure
Jordan, J. B., Poppe, L., Haniu, M., Arvedson, T., Syed, R., Li, V., Kohno, H., Kim, H., Schnier, P. D., Harvey, T. S., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.017764 · Cited by 214
Du, X., Volkov, O. A., Czerwinski, R. M., Tan, H., Huerta, C., Morton, E. R., Rizzi, J. P., Wehn, P. M., Xu, R., Nijhawan, D., et al. (2019) · Structure · doi:10.1016/j.str.2019.10.005 · Cited by 181
Crystal structure of a membrane-embedded H+-translocating pyrophosphatase
Lin, S.-M., Tsai, J.-Y., Hsiao, C.-D., Huang, Y.-T., Chiu, C.-L., Liu, M.-H., Tung, J.-Y., Liu, T.-H., Pan, R.-L., & Sun, Y.-J. (2012) · Nature · doi:10.1038/nature10963 · Cited by 156
PCNA directs type 2 RNase H activity on DNA replication and repair substrates
Bubeck, D., Reijns, M. A. M., Graham, S. C., Astell, K. R., Jones, E. Y., & Jackson, A. P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq980 · Cited by 144
Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria
Luo, X., Fu, G., Wang, R. E., Zhu, X., Zambaldo, C., Liu, R., Liu, T., Lyu, X., Du, J., Xuan, W., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2405 · Cited by 134
The second messenger c-di-AMP inhibits the osmolyte uptake system OpuC in Staphylococcus aureus
Schuster, C. F., Bellows, L. E., Tosi, T., Campeotto, I., Corrigan, R. M., Freemont, P., & Gründling, A. (2016) · Science Signaling · doi:10.1126/scisignal.aaf7279 · Cited by 109
Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice
Guo, S., Stevens, C. A., Vance, T. D. R., Olijve, L. L. C., Graham, L. A., Campbell, R. L., Yazdi, S. R., Escobedo, C., Bar-Dolev, M., Yashunsky, V., et al. (2017) · Science Advances · doi:10.1126/sciadv.1701440 · Cited by 107
Warne, J., Pryce, G., Hill, J. M., Shi, X., Lennerås, F., Puentes, F., Kip, M., Hilditch, L., Walker, P., Simone, M. I., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.700385 · Cited by 99
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis
Chim, N., Iniguez, A., Nguyen, T. Q., & Goulding, C. W. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.11.025 · Cited by 102
Lorca, G. L., Ezersky, A., Lunin, V. V., Walker, J. R., Altamentova, S., Evdokimova, E., Vedadi, M., Bochkarev, A., & Savchenko, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m610838200 · Cited by 87
Yin and yang regulation of stress granules by Caprin-1
Song, D., Kuang, L., Yang, L., Wang, L., Li, H., Li, X., Zhu, Z., Shi, C., Zhu, H., & Gong, W. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207975119 · Cited by 72
Yu, Y., Xu, F., Zhao, W., Thoma, C., Che, S., Richman, J. E., Jin, B., Zhu, Y., Xing, Y., Wackett, L., et al. (2024) · Science Advances · doi:10.1126/sciadv.ado2957 · Cited by 63
Mas-y-Mas, S., Barbon, M., Teyssier, C., Déméné, H., Carvalho, J. E., Bird, L. E., Lebedev, A., Fattori, J., Schubert, M., Dumas, C., et al. (2016) · PLOS ONE · doi:10.1371/journal.pone.0165139 · Cited by 43
Self-citationCa2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.
Vance, T. D. R., Olijve, L. L. C., Campbell, R. L., Voets, I. K., Davies, P. L., & Guo, S. (2014) · Bioscience Reports · doi:10.1042/bsr20140083 · Cited by 40
Design of high-affinity binders to immune modulating receptors for cancer immunotherapy
Yang, W., Hicks, D. R., Ghosh, A., Schwartze, T. A., Conventry, B., Goreshnik, I., Allen, A., Halabiya, S. F., Kim, C. J., Hinck, C. S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57192-z · Cited by 40
Ranking power of the SQM/COSMO scoring function on carbonic anhydrase II-inhibitor complexes.
Pecina, A., Brynda, J., Vrzal, L., Gnanasekaran, R., Hořejší, M., Eyrilmez, S. M., Řezáč, J., Lepšík, M., Řezáčová, P., Hobza, P., et al. (2018) · ChemPhysChem · doi:10.1002/cphc.201701104 · Cited by 36
Structural and functional characterization of Schistosoma mansoni Thioredoxin
Boumis, G., Angelucci, F., Bellelli, A., Brunori, M., Dimastrogiovanni, D., & Miele, A. E. (2011) · Protein Science · doi:10.1002/pro.634 · Cited by 23
Photocobilins integrate B12 and bilin photochemistry for enzyme control
Zhang, S., Jeffreys, L. N., Poddar, H., Yu, Y., Liu, C., Patel, K., Johannissen, L. O., Zhu, L., Cliff, M. J., Yan, C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46995-1 · Cited by 13
Unravelling the Adaptation Mechanisms to High Pressure in Proteins
Caliò, A., Dubois, C., Fontanay, S., Koza, M. M., Hoh, F., Roumestand, C., Oger, P., & Peters, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23158469 · Cited by 12
A fully automated benchmarking suite to compare macromolecular complexes
Studer, G., Robin, X., Bienert, S., Durairaj, J., Škrinjar, P., Tauriello, G., Waterhouse, A. M., & Schwede, T. (2026) · Nature Methods · doi:10.1038/s41592-025-02973-z · Cited by 10
“Amino acid and nucleotide parameters are now extracted from the CCP4 MON_LIB 65 instead of the previously used amino acid parameters from ref.”
Feng, Y., Yang, X., Ji, H., Deng, Z., Lin, S., & Zheng, J. (2022) · Communications Biology · doi:10.1038/s42003-022-03477-8 · Cited by 9
Dixon, T., MacPherson, D., Mostofian, B., Dauzhenka, T., Lotz, S., McGee, D., Shechter, S., Shrestha, U. R., Wiewiora, R., McDargh, Z. A., et al. (2021) · doi:10.1101/2021.09.26.461830 · Cited by 7
Engineering of soluble bacteriorhodopsin
Nikolaev, A., Orlov, Y., Tsybrov, F., Kuznetsova, E., Shishkin, P., Kuzmin, A., Mikhailov, A., Nikolaeva, Y. S., Anuchina, A., Chizhov, I., et al. (2025) · Chemical Science · doi:10.1039/d5sc02453f · Cited by 6
Yu, Y., Xu, F., Zhao, W., Thoma, C., Che, S., Richman, J. E., Jin, B., Zhu, Y., Xing, Y., Wackett, L., et al. (2023) · doi:10.1101/2023.12.13.568471 · Cited by 4
Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus
Burmeister, W. P., Boutin, L., Balestra, A. C., Gröger, H., Ballandras-Colas, A., Hutin, S., Kraft, C., Grimm, C., Böttcher, B., Fischer, U., et al. (2024) · PLOS Pathogens · doi:10.1371/journal.ppat.1011652 · Cited by 3
Metadata
- Authors
- Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F., & Murshudov, G. N.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2004-11-26
- Volume
- 60
- Issue
- 12
- Pages
- 2184-2195
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2119489910
- Cited by
- 1,350
- References
- 2
- FWCI
- 4.79
- 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.
