Dali server update

By Liisa Holm, Laura M. Laakso. 2016

908 citations recorded by the source corpus.

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, positive): “We used DALI 43 to screen for structure homologues to both the known and putative alternative Mpt53 structure.”
DALI and the persistence of protein shape (2019, background): “24 The first use of these dendrograms was in a study on the multiple origins of viral capsid proteins from cellular ancestors.”
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures (2019, background): “The domain page also provides a set of links to external resources such as CATH (15), ECOD (16), Protein contacts atlas (18), PDBe-KB and PDBe-PISA (19) as well as a range of resources for structure comparison and searches such as DALI (20), FATCAT (21), TOPMATCH (22) and PDBe-Fold (19) allowing use”
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.biocenter.helsinki.fi/dali).”