DALI 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 IN pipelines

 (18)
2017
PMCID: 5651945
PMID: 29057942
DOI: 10.1038/s41598-017-13288-1

[…] the combined structure was then built and refined using refmac34 and coot35. data collection and refinement statistics are summarised in table 2. structural alignments were performed with the dali server36, manually edited and presented with espript37. figures were generated using pymol (http://www.pymol.org).table 2 data collection space group p41212cell dimensions a, b, c (å)74.32, […]

2016
PMCID: 4999995
PMID: 27562564
DOI: 10.1038/srep32070

[…] 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 […]

2016
PMCID: 5131608
PMID: 27612581
DOI: 10.1016/j.jsb.2016.08.006

[…] from tt122238-123 in tt121836-123., we used the protein structure comparison service pdbefold at the european bioinformatics institute (krissinel and henrick, 2004), hhpred (soding et al., 2005) and dali (holm and rosenstrom, 2010) to search for pilins with similar folds (table 4). the closest structure identified was the type ii secretion pseudopilin epsi (pdb 3cfi) from vibrio vulnificus, […]

2015
PMCID: 4546622
PMID: 26296208
DOI: 10.1371/journal.pone.0136239

[…] institute [23]. analysis of the structure was assisted by output from the pdbsum generate webserver [24,25] and database searches for structural homologues to ktr4p were performed with dali [26]. figures were prepared in pymol [27]., the transfer activity of ktr4p was determined in vitro using the glycosyltransferase activity kit from r&d systems, following the instructions […]

2015
PMCID: 4599027
PMID: 26449279
DOI: 10.1186/s12900-015-0046-0

[…] of diplonema, we computed a score measuring 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 […]

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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