The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
DALI and the persistence of protein shape
Open accessAbstract
DALI is a popular resource for comparing protein structures. The software is based on distance‐matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta‐analysis of independent reference‐based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
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The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602
Protein Structure Comparison by Alignment of Distance Matrices
Holm, L., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1489 · Cited by 3,984 · cited 2×
“20 The heuristics reduce protein structure to ungapped secondary structure elements to simplify the combinatorial search.”
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Structure, lipid scrambling activity and role in autophagosome formation of ATG9A
Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C. M., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., & Otomo, T. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00520-2 · Cited by 305
Kunisch, F., Campobasso, C., Wagemans, J., Yildirim, S., Chan, B. K., Schaudinn, C., Lavigne, R., Turner, P. E., Raschke, M. J., Trampuz, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52595-w · Cited by 101
Lee, S. C., Adams, D. W., Ipsaro, J. J., Cahn, J., Lynn, J., Kim, H.-S., Berube, B., Major, V., Calarco, J. P., LeBlanc, C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.001 · Cited by 89
Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · doi:10.1101/2021.05.10.443524 · Cited by 89
Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation
Linares, R., Arnaud, C.-A., Effantin, G., Darnault, C., Epalle, N. H., Boeri Erba, E., Schoehn, G., & Breyton, C. (2023) · Science Advances · doi:10.1126/sciadv.ade9674 · Cited by 75
Metadata
- Authors
- Holm, L.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2019-11-05
- Volume
- 29
- Issue
- 1
- Pages
- 128-140
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- OpenAlex
- W2980170804
- Cited by
- 692
- References
- 4
- FWCI
- 27.57
- Type
- journal article
- Language
- en
- Open access
- green
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