The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
DALI shines a light on remote homologs: One hundred discoveries
Open accessAbstract
Structural comparison reveals remote homology that often fails to be detected by sequence comparison. The DALI web server (http://ekhidna2.biocenter.helsinki.fi/dali) is a platform for structural analysis that provides database searches and interactive visualization, including structural alignments annotated with secondary structure, protein families and sequence logos, and 3D structure superimposition supported by color‐coded sequence and structure conservation. Here, we are using DALI to mine the AlphaFold Database version 1, which increased the structural coverage of protein families by 20%. We found 100 remote homologous relationships hitherto unreported in the current reference database for protein domains, Pfam 35.0. In particular, we linked 35 domains of unknown function (DUFs) to the previously characterized families, generating a functional hypothesis that can be explored downstream in structural biology studies. Other findings include gene fusions, tandem duplications, and adjustments to domain boundaries. The evidence for homology can be browsed interactively through live examples on DALI's website.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · cited 3×
“A total of 59% of the Pfam families are represented in AlphaFold Database version 1 (AFDB1), which covers the human proteome as well as the proteomes of other important model organisms (Varadi et al., 2022).”
BackgroundMethodInfluentialFast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2022) · doi:10.1101/2022.02.07.479398 · Cited by 2,598
Fast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01773-0 · Cited by 2,596
The InterPro protein families and domains database: 20 years on
Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa977 · Cited by 2,231
HH-suite3 for fast remote homology detection and deep protein annotation
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., & Söding, J. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3019-7 · Cited by 1,145
High‐accuracy protein structure prediction in CASP14
Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26171 · Cited by 314 · cited 2×
“The predicted AlphaFold models are remarkably accurate, displaying low RMSD values and high Z-scores, and add to the record of successful predictions by AlphaFold (Jumper et al., 2021; Pereira et al., 2021) (Table 1).”
BackgroundResultLarge-scale investigation of the reasons why potentially important genes are ignored
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Cited by
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
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Metadata
- Authors
- Holm, L., Laiho, A., Törönen, P., & Salgado, M.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2022-12-19
- Volume
- 32
- Issue
- 1
- Pages
- e4519-e4519
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- OpenAlex
- W4309858927
- Cited by
- 696
- References
- 10
- FWCI
- 36.53
- Type
- journal article
- Language
- en
- Open access
- green
- Funders
- Novo Nordisk Fonden (NNF200C0065157)
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