DALI and the persistence of protein shape

By Liisa Holm. 2019

618 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins (2021, methodology): “The structural tree of the Acr proteins was generated from distance matrices, where the pseudo-distance between two structures Q and T was deﬁned as [48]: The hierarchical clustering of the similarity matrix was outputted as a Newick format-ted dendrogram.”
DALI shines a light on remote homologs: One hundred discoveries (2022, methodology): “The user interface has been described previously (Holm, 2020; Holm & Laakso, 2016) and tutorials are available on the website (http://ekhidna2.”
A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2 (2022, methodology): “The final predicted domain structures were submitted to the Dali server (Holm, 2020) to identify the closest structural homologs in the PDB.”
Structural basis of WLS/Evi-mediated Wnt transport and secretion (2020, methodology): “A search of the Protein Database with the WLS TM domain using the DALI server (Holm, 2020) identified GPCRs including Smoothened (PDB ID 6D35 and 6O3C) (Deshpande et al., 2019; Huang et al., 2018), Frizzled 4 (PDB ID 6BD4) (Yang et al., 2018) and the glucagon receptor (PDB ID 5YQZ) (Zhang et al.,…”
Dali server: structural unification of protein families (2022, positive): “Dali structure comparison has been shown to outperform other methods in the sensitivity of detecting similar folds in the twilight or midnight zones of sequence similarity (15,19,28).”
Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2 (2022, methodology): “The final predicted domain structures were submitted to the Dali server [43] to identify the closest structural homologs in the PDB.”