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The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework
Abstract
The advent of structural genomics initiatives has led to a pressing need for high-throughput macromolecular structure determination. To accomplish this, new methods and inevitably new software must be developed to accelerate the process of structure solution. To minimize duplication of effort and to generate maintainable code efficiently, a toolbox of basic crystallographic software components is required. The development of the Computational Crystallography Toolbox(cctbx) has been undertaken for this purpose. In this paper, the fundamental requirements for the cctbx are outlined and the decisions that have lead to its implementation are explained. The cctbx currently contains algorithms for the handling of unit cells, space groups and atomic scatterers, and is released under an Open Source license to allow unrestricted use and continued development. It will be developed further to become a comprehensive library of crystallographic tools useful to the entire community of software developers.
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Cited by
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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
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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
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
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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
Self-citationMolProbity: 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
Self-citationPHENIX : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361
Self-citationLikelihood-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
Sequence-assignment validation in cryo-EM models with checkMySequence
Chojnowski, G. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322005009 · Cited by 20
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Metadata
- Authors
- Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W., & Adams, P. D.
- Venue
- Journal of Applied Crystallography
- Published
- 2002-01-22
- Volume
- 35
- Issue
- 1
- Pages
- 126-136
- ISSN
- 0021-8898 (ISSN-L)
- OpenAlex
- W2116389515
- Cited by
- 289
- References
- 0
- FWCI
- 3.98
- Type
- journal article
- Language
- en
- Open access
- closed
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