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DaliLite specifications

Information


Unique identifier OMICS_06825
Name DaliLite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Information


Unique identifier OMICS_06825
Name DaliLite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for DaliLite

DaliLite in pipelines

 (18)
2018
PMCID: 5919458
PMID: 29698445
DOI: 10.1371/journal.pone.0196349

[…] were performed using the pymol package []. structure comparisons were performed using the fatcat algorithm [] included in the protein comparison tool of the protein data bank (pdb) web server. dalilite v3 was used to search for structural related proteins []., the available crystal structures of the hisf, purm, and their paralogues were retrieved from the pdb. a total of 38 structures […]

2017
PMCID: 5512222
PMID: 28559295
DOI: 10.1128/JB.00245-17

[…] parameters for clustering of nearly identical proteins were l = 0.9 and s = 1.2. the hhpred program was used for profile-profile searches (). structure similarity searches were performed with the dalilite program (, ). multiple-sequence alignments were built by the kalign () and pcma () programs, followed by manual adjustments on the basis of profile-profile and structural alignments. […]

2017
PMCID: 5622079
PMID: 28963468
DOI: 10.1038/s41467-017-00785-0

[…] with 32% sequence identity and 89% sequence coverage. the cp1 domain model was then replaced by the crystal structure of human lrs cp1 domain (pdb 2wfda) by superimposition using the pairwise dalilite server. the model prediction of the c-terminal une-l domain was performed by robetta online rosetta server using chain a of linear ubiquitin and antibody fab fragment complex crystal […]

2015
PMCID: 4326362
PMID: 25644171
DOI: 10.1186/s12964-015-0087-9

[…] was done using the modeller program []. structural manipulations, surface topology studies, and graphical representations were performed using arguslab (thompson, planaria software), vmd [], and dalilite v3 []. the extensive energy minimization was done using deep view []. structural constraints and prediction quality of the modeled structures were evaluated using whatif [] and procheck []., […]

2015
PMCID: 4470068
PMID: 26136688
DOI: 10.3389/fphys.2015.00180

[…] mad2a was retrieved from the protein data bank (pdb id: 1klq; doi: 10.2210/pdb1klq/pdb). the structural identities were assigned to the multiple sequence data using the protein structure database dalilite ver. 3.0 (holm and rosenstrom, )., the evolutionary position of the tmatg13 n- terminal horma domain was analyzed with respect to its orthologs using the maximum likelihood method based […]


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DaliLite in publications

 (189)
PMCID: 5895030
PMID: 29641586
DOI: 10.1371/journal.pone.0195559

[…] of one of the identified proteins (harxl23 []) and avre1 from p. syringae using the iterative threading assembly refinement (i-tasser [–]), and compared their structural similarity using the dalilite [] method. based on this similarity, we hypothesized that avre1 and harxl23 may have convergently evolved to perturb the same host target(s). as an initial test of this hypothesis, […]

PMCID: 5823473
PMID: 29425238
DOI: 10.1371/journal.ppat.1006850

[…] tbaldh3 refinement. figures were prepared using pymol (schrödinger llc). the dali server was used to search the pdb for structural homologues and structural superpositions were performed using dalilite []. multiple sequence alignments were calculated using clustalw2 [] and edited using aline []. crystallographic statistics are presented in ., an3057, […]

PMCID: 5775757
PMID: 29372122
DOI: 10.7717/peerj.4288

[…] modelling of abd, was the actin-binding domain of schizosaccharomyces pombe α-actinin. although the sequence of bigelowiella abd is only ca 39% identical to the abd of s pombe (pdb: 5bvr), the dalilite server () returns a very high z-score of 32.5 and a low root mean deviation value of 1.0 å. when the dali server was interrogated with bigelowiella abd as query structure, several structures […]

PMCID: 5622079
PMID: 28963468
DOI: 10.1038/s41467-017-00785-0

[…] with 32% sequence identity and 89% sequence coverage. the cp1 domain model was then replaced by the crystal structure of human lrs cp1 domain (pdb 2wfda) by superimposition using the pairwise dalilite server. the model prediction of the c-terminal une-l domain was performed by robetta online rosetta server using chain a of linear ubiquitin and antibody fab fragment complex crystal […]

PMCID: 5595797
PMID: 28900273
DOI: 10.1038/s41598-017-11542-0

[…] into the protein data bank (pdb) with the accession number (5wut)., structural analysis was carried out using a set of programs: dali was used for the search of similar structures from the database, dalilite was used for the superposition of molecules, espript was used for the preparation of alignment figures, and pymol (http://pymol.sourceforge.net/) for the depiction of structures., we failed […]


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