DALI protocols

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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

 (33)
2018
PMCID: 5774825
PMID: 29352301
DOI: 10.1371/journal.pone.0191610

[…] and the adit validation server (http://deposit.pdb.org/validate/). coordinates have been deposited within the protein data bank as pdb file 4j2o. structural homologs for ab-wbjb were identified with dali searches [], last accessed in august 2017. all molecular views presented here were prepared using pymol []., to generate mutants m134a-wbjb and m134y-wbjb, isolated pet15b plasmids harbouring […]

2018
PMCID: 5862659
PMID: 29198957
DOI: 10.1016/j.jmb.2017.11.014

[…] returned similar models having identical fold. in addition, models were evaluated with prosa-web (table s2). top scoring models were used for further analyses. structures were aligned using either dali or the “cealign” command in pymol., covariation analysis was performed using psicov and plmc script from evmutation package . initial sequence alignment was generated by jackhmmer after 10 […]

2018
PMCID: 5871717
PMID: 29551265
DOI: 10.1016/j.cell.2018.02.032

[…] tetramer was refined in haddock (), in order to optimize the molecular geometry., structural figures and animations were generated with pymol (schrödinger); sequence alignments were generated with dali () and espript (). protein interfaces were analyzed in pisa (), protein-dna contacts in nucplot () and dna parameters in 3dna ()., reaction products from strand exchange assays with int82n, […]

2017
PMCID: 5216131
PMID: 28045099
DOI: 10.1038/ncomms14128

[…] care and use committee (thomas jefferson university)., a homology model of dfna5 was generated using the swiss-model server. structural homologues were identified in the rcsb database using the dali server. structural superimpositions were carried out in coot and chimera. all ribbon diagrams presented in the paper were prepared using the program pymol (delano, w.l. the pymol molecular […]

2017
PMCID: 5233953
PMID: 28084396
DOI: 10.1038/srep40408

[…] surface, frpd was protonated according to ph 7.4. the maximum esp for the colour range was 100 kcal/mol. comparative structure-based homology analysis of the frpd structure was carried out using dali, cath, and pdbefold. figures were prepared with pymol (http://www.pymol.org)., saxs data were collected on the beamline x33 embl at doris-iii in hamburg, germany. the concentrations of frpd […]


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DALI in publications

 (808)
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] further advance the understanding of endos glycan specificity, we performed a structural analysis in the context of the gh18 family of endoglycosidases. a search for structural homologues using the dali server revealed five endoglycosidases of the gh18 family with significant structural similarity to endos: (i) endof3 from elizabethkingia meningoseptica (pdb code 1eom; dali z-score of 21.9; […]

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, […]

PMCID: 5934362
PMID: 29725056
DOI: 10.1038/s41598-018-25171-8

[…] 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. […]

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

[…] of human angptl3 and angptl4 share significant sequence and structural homology with other fibrinogen-like domains. angptl3 can be superimposed on its closest structural homologues, identified by dali server, angiopoietins 1 and 2 with a rms deviation of 2.3 å (192 equivalent cα positions; 4jyo) or 2.4 å (192 equivalent cα positions; 1z3s) respectively. similarly angiopoietins 1 and 2 […]

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

[…] expected values with mean h bond energy (-1.6 sd = 0.5) 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. […]


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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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