Dali server: conservation mapping in 3D

By Liisa Holm, Päivi Rosenström. 2010

3,792 citations recorded by the source corpus.

Our web site (http://ekhidna.biocenter.helsinki.fi/dali_server) runs the Dali program for protein structure comparison. The web site consists of three parts: (i) the Dali server compares newly solved structures against structures in the Protein Data Bank (PDB), (ii) the Dali database allows browsing precomputed structural neighbourhoods and (iii) the pairwise comparison generates suboptimal alignments for a pair of structures. Each part has its own query form and a common format for the results page. The inputs are either PDB identifiers or novel structures uploaded by the user. The results pages are hyperlinked to aid interactive analysis. The web interface is simple and easy to use. The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how conserved residues and ligands cluster together in multiple structure superimpositions. In favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold (2016, methodology): “The DALI server (13) was used to search the Protein Data Bank to identify known structures with similar folds to LmFH-2.”
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex (2022, background): “We identified two of the subunits of the BLOC-2 complex–HPS3 and HPS5–in our Dali search (Figure 6—figure supplement 1), as being structurally similar to IFT-A proteins.”
The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments (2013, neutral): “The comparative structural analysis using the Dali server (Holm and Rosenström, 2010; http://ekhidna.biocenter.helsinki.fi/dali_server) demonstrated that KaiB molecule bears strong resemblance to the thioredoxin family protein structures.”
A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, methodology): “We thus used the Dali server (Holm and Rosenström, 2010) to identify structures that have been resolved in the presence of a protein ligand and that most closely resembles the APBB1-PTB1 domain.”
mTM-align: a server for fast protein structure database search and multiple protein structure alignment (2018, methodology): “If hits are found, a procedure called ‘walk’ (please note that the name and the idea of walk were from the Dali server papers (2,13)) is used to find more similar structures in NRDB (introduced in the next para-graph).”
The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain (2014, background): “fi/dali server/start) to perform a search against the ATPase core of RIG-I (PDB 4A36) (13,53).”
MMDB and VAST+: tracking structural similarities between macromolecular complexes (2013, methodology): “DALI was one of the first structure comparison methods that relied solely on geometric criteria and has been available since themid 1990s.”
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA (2014, background): “A Dali search (Holm and Rosenstrom, 2010) revealed that the REC lobe does not share structural similarity with other known proteins, indicating that it is a Cas9-specific functional domain.”
Structure of the Plasmodium 6-cysteine s48/45 domain (2012, methodology): “Structure similarity searches using the DaliLite (43) program indicate that the β-sandwich fold shared by s48/45 and the SRS superfamily is further related to comparable β-sandwich domains found in a diverse array of cellsurface molecules from various organisms (z > 4 in reciprocal structure similar”
Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. (2016, methodology): “To examine whether the structure of bactofilin we determined provides clues as to potential eukaryotic homologs, we used both DALI (41) and deconSTRUCT (42) to search for structural homologs.”