The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps
Open accessAbstract
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps.ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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
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
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
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
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
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
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005659 · Cited by 2,748
Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J., & Adams, P. D. (2008) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490705024x · Cited by 1,462
Research works printed but not linked: 39
- Afonine, P. V., Klaholz, B. P., Moriarty, N. W., Poon, B. K., Sobolev, O. V., Terwilliger, T. C., Adams, P. D. & Urzhumtsev, A. (2018). bioRxiv, https://doi.org/10.1101/279844. · DOI
- Brändén, 1990, Nature (London), 343, 687, 10.1038/343687a0 · DOI · Paper page
- Brereton, 2016, Protein Sci., 25, 926, 10.1002/pro.2883 · DOI
- Brünger, A. T. (1992). X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. New Haven: Yale University Press.
- Chen, 2009, Protein Sci., 18, 2403, 10.1002/pro.250 · DOI
- Conti, F., Barbagli, F., Balaniuk, R., Halg, M., Lu, C., Morris, D., Sentis, L., Vileshin, E., Warren, J., Khatib, O. & Salisbury, K. (2003). EuroHaptics 2003: Proceedings, edited by I. Oakley, S. O'Modhrain & F. Newell, pp. 496-500. Dublin: Media Lab.
- Cowtan, 2006, Acta Cryst. D, 62, 1002, 10.1107/S0907444906022116 · DOI · Paper page
- Croll, 2015, Acta Cryst. D, 71, 706, 10.1107/S1399004715000826 · DOI
- Croll, 2016, Acta Cryst. D, 72, 1006, 10.1107/S2059798316012201 · DOI
- Croll, 2016, Structure, 24, 469, 10.1016/j.str.2015.12.014 · DOI
- Focht, 2017, Front. Physiol., 8, 202, 10.3389/fphys.2017.00202 · DOI
- Goddard, 2017, Protein Sci., 27, 14, 10.1002/pro.3235 · DOI · Paper page
- Hintze, 2016, Proteins, 84, 1177, 10.1002/prot.25039 · DOI
- Hooft, 1996, Nature (London), 381, 272, 10.1038/381272a0 · DOI
- Joosten, 2012, Acta Cryst. D, 68, 484, 10.1107/S0907444911054515 · DOI
- Joosten, 2014, IUCrJ, 1, 213, 10.1107/S2052252514009324 · DOI · Paper page
- Joseph, 2016, Methods, 100, 42, 10.1016/j.ymeth.2016.03.007 · DOI
- Kirmizialtin, 2015, Methods Enzymol., 558, 497, 10.1016/bs.mie.2015.02.011 · DOI
- Kleywegt, 2000, Acta Cryst. D, 56, 249, 10.1107/S0907444999016364 · DOI
- Kleywegt, 1995, Structure, 3, 535, 10.1016/S0969-2126(01)00187-3 · DOI
- Langer, 2008, Nature Protoc., 3, 1171, 10.1038/nprot.2008.91 · DOI · Paper page
- Laskowski, 1998, Curr. Opin. Struct. Biol., 8, 631, 10.1016/S0959-440X(98)80156-5 · DOI
- Li, 2015, J. Phys. Chem. B, 119, 883, 10.1021/jp505875v · DOI · Paper page
- Li, 2015, Nature (London), 524, 186, 10.1038/nature14685 · DOI · Paper page
- Maier, 2015, J. Chem. Theory Comput., 11, 3696, 10.1021/acs.jctc.5b00255 · DOI · Paper page
- McNicholas, 2017, Protein Sci., 27, 207, 10.1002/pro.3299 · DOI
- McNicholas, 2011, Acta Cryst. D, 67, 386, 10.1107/S0907444911007281 · DOI · Paper page
- Murshudov, 2011, Acta Cryst. D, 67, 355, 10.1107/S0907444911001314 · DOI · Paper page
- Nguyen, 2013, J. Chem. Theory Comput., 9, 2020, 10.1021/ct3010485 · DOI · Paper page
- Perez, 2015, J. Chem. Theory Comput., 11, 4770, 10.1021/acs.jctc.5b00662 · DOI
- Read, 2011, Structure, 19, 1395, 10.1016/j.str.2011.08.006 · DOI · Paper page
- Rode, 2005, Coord. Chem. Rev., 249, 2993, 10.1016/j.ccr.2005.03.032 · DOI
- Stein, 2008, J. Appl. Cryst., 41, 641, 10.1107/S0021889808006985 · DOI · Paper page
- Stewart, 1990, J. Mol. Biol., 214, 253, 10.1016/0022-2836(90)90159-J · DOI
- Touw, 2015, Acta Cryst. D, 71, 1604, 10.1107/S1399004715008263 · DOI
- Touw, 2016, Acta Cryst. D, 72, 1110, 10.1107/S2059798316013036 · DOI
- Trabuco, 2008, Structure, 16, 673, 10.1016/j.str.2008.03.005 · DOI · Paper page
- Wang, 2016, Elife, 5, e17219, 10.7554/eLife.17219 · DOI · Paper page
- Wlodawer, 2013, FEBS J., 280, 5705, 10.1111/febs.12495 · DOI
Cited by
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897
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-citationStructure-based design of prefusion-stabilized SARS-CoV-2 spikes
Hsieh, C.-L., Goldsmith, J. A., Schaub, J. M., DiVenere, A. M., Kuo, H.-C., Javanmardi, K., Le, K. C., Wrapp, D., Lee, A. G., Liu, Y., et al. (2020) · Science · doi:10.1126/science.abd0826 · Cited by 1,303
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike
Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J. F.-W., Sahi, V., Figueroa, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2571-7 · Cited by 1,349
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901
Metadata
- Authors
- Croll, T. I.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2018-04-11
- Volume
- 74
- Issue
- 6
- Pages
- 519-530
- ISSN
- 2059-7983 (ISSN-L)
- OpenAlex
- W2801376357
- Cited by
- 2,038
- References
- 7
- FWCI
- 25.66
- Type
- journal article
- Language
- en
- Open access
- hybrid
- Licence
- creativecommons.org/licenses/by/2.0/uk/legalcode (vor)
- creativecommons.org/licenses/by/2.0/uk/legalcode (tdm)
- Funders
- Wellcome Trust (082961/Z/07/Z)
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. https://app.cochat.ai/papers/10.1107/s2059798318002425
- The paper
- Croll, T. I. (2018). ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallographica Section D Structural Biology. https://doi.org/10.1107/s2059798318002425
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.
