DALI pipeline

DALI specifications


Unique identifier OMICS_03645
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



  • person_outline Liisa Holm <>
  • person_outline Voytek Kasprzak <>

Publications for DALI


Dali server update.

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

DALI citations

PMCID: 4999995

[…] ring-like cross-braced binuclear tc fold. these domains lack the typical ‘squiggle’ and instead have an extended region after the core α-helix that contributes residues to bind the second metal ion. dali structure similarity search with b-box (pdbid 3q1d_a) could retrieve ring domain of baculoviral iap repeat-containing protein 7 (pdbid 4auq_b; z-score = 3.6, rmsd = 2.0 å, nali = 39) and ffas […]

PMCID: 4614863

[…] contact with the roq domain. this six-helix bundle was found to resemble an hepn (higher eukaryotes and prokaryotes nucleotide-binding) domain based on a structural homologue search of rc3h1 using dali9 (fig. 1b). the hepn domain of rc3h2 superimposes with that of rc3h1 with a root mean squared deviation (rmsd) of 0.52 å for all atoms in 145 residues. an examination of the rc3h2 hepn structure […]

PMCID: 4599027

[…] how unexpected each residue of the protein is. using the i-tasser model of dprnl as the query structure, we searched for structural “neighbors” with dali (http://ekhidna.biocenter.helsinki.fi/dali_server/, [59]): we selected 23 unique rna and dna ligases whose structure have the highest percentage of identity and the lowest root mean square deviation (rmsd), and performed a multiple […]

PMCID: 4449002

[…] and 1c, right panel). the secondary structure observed in the structure is consistent with nmr secondary chemical shifts (fig 2a). structural similarity searches in the protein data bank (pdb) using dali and pdbefold did not identify any structures with a similar fold (see experimental methods for details). thus, the n-terminal domain of ebna-2 represents a novel dimerization fold, […]

PMCID: 4335047

[…] of s. cerevisiae asprs-trnaasp complex (pdb: 1asz[ref: pubmed: 8313877]) was aligned with t. cruzi hisrs (pdb: 3hrk) by superimposing the highly conserved catalytic core domain (327 residues) using dali pairwise comparison with default parameters [ref: pubmed: 19481444]. this alignment produced a robust z score of 12.9, a rmsd of 3.0 å, and minimal clashes between trnaasp and hisrs. a similar […]

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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