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Protocols

DALI specifications

Information


Unique identifier OMICS_03645
Name DALI
Alternative names DaliLite, Dali server
Interface Web user interface
Restrictions to use None
Input data One or more protein structures in PDB format. The query structure can be specified as a PDB identifier plus chain identifier, or a PDB file uploaded by the user. All backbone atoms (N, CA, C, O) are required and the minimum chain length is 30 amino acids. If only the amino sequence is known, it can be mapped to the closest known structure by a sequence similarity search against PDB.
Output data PDB search, pairwise comparison and all-against-all comparison produce summaries of structural neighbours in a common output format and share interactive analysis tools.
Output format PDB,
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Liisa Holm
  • person_outline Voytek Kasprzak

Publications for DALI

library_books

Dali server update

2016 Nucleic Acids Res
PMCID: 4987910
PMID: 27131377
DOI: 10.1093/nar/gkw357

DALI citations

 (1187)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] Structure based sequence alignment analysis were performed using Chimera. Protein pocket volume was calculated using HOLLOW. Z-score values were produced by using DALI. Domain interface analysis was performed using PISA. Conserved and similar residues were labeled using BoxShade server (http://embnet.vital-it.ch/software/BOX_form.html). […]

library_books

Structure and mechanism of the two component α helical pore forming toxin YaxAB

2018
Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] α1-α6 (Fig. , helices with bold black outline). We found striking similarities between both head domains, with all structurally elucidated members from the wider ClyA family of α-PFTs, by performing DALI analysis (Supplementary Figure  and Supplementary Figure ). For alignments of the YaxA head domain, Z-scores ranged from 9.6 (soluble-monomeric ClyA, 5.5 Å RMSD; PDB code 1QOY) to 12.2 (NheA, 3.4 […]

call_split

Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin dockerin interaction

2018
Sci Rep
PMCID: 5934362
PMID: 29725056
DOI: 10.1038/s41598-018-25171-8
call_split See protocol

[…] tion was found using a cohesin from R. flavefaciens strain 17 ScaB (unreleased) and an ensemble of 3 R. flavefaciens FD-1 dockerins (Doc1a from 5M2O, Doc1b from 5M2S and Doc3 from 5LXV) produced with Dali. The cohesin had a sequence identity of 33.0% and the dockerins between 22% (Doc3) and 34% (Doc1b). Two copies of the heterodimer RfCohScaB5-DocScaA complex were present in the asymmetric unit. T […]

library_books

Identification of a pyrophosphate dependent kinase and its donor selectivity determinants

2018
Nat Commun
PMCID: 5931981
PMID: 29720581
DOI: 10.1038/s41467-018-04201-z

[…] tified based on structural similarity to a myo-inositol 3-kinase from the hyperthermophilic archaeon Thermococcus kodakarensis (MI3K_TK), which is an ATP-dependent member of the ribokinase family,. A Dali search with the substrate-complex structure of MI3K_TK (Protein Data Bank (PDB) ID 4XF7) showed that the structure is the most similar to the unliganded structure of TM0415 from the hyperthermoph […]

library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] 5) against the expected score values of -2.0 (SD = 0.8). The secondary structure assignment of the functional WRKY protein was analyzed using the DALI web server (http://ekhidna.biocenter.helsinki.fi/dali_server/start) []. The DALI results revealed that in the functional protein sequence 40.84% residues occupied or constituted the β strands. However, some residues in the functional protein such as […]

library_books

Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease

2018
Sci Rep
PMCID: 5928061
PMID: 29713054
DOI: 10.1038/s41598-018-25237-7

[…] ructures and β-strand β6 is much shorter and turns away from the β-sheet towards the solvent and together with β7, α5 and an extended loop creates a separate solvent exposed element in the structure. DALI searches using just the P subdomain of Angptl3 or Angptl4 revealed no close structural homologs.Figure 2In contrast to Angiopoietin family members and other identified structural homologs, includ […]

Citations

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DALI institution(s)
Institute of Biotechnology, University of Helsinki, Finland; Department of Biosciences, University of Helsinki, Finland
DALI funding source(s)
Supported by Biocenter Finland.

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