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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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Highly accurate protein structure prediction with AlphaFold
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“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
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Fast and accurate protein structure search with Foldseek
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“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).”
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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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