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Protocols

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


No version available

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 citations

 (68)
library_books

Host parasite co metabolic activation of antitrypanosomal aminomethyl benzoxaboroles

2018
PLoS Pathog
PMCID: 5823473
PMID: 29425238
DOI: 10.1371/journal.ppat.1006850

[…] during 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 . […]

call_split

Laminarinase from Flavobacterium sp. reveals the structural basis of thermostability and substrate specificity

2017
Sci Rep
PMCID: 5595797
PMID: 28900273
DOI: 10.1038/s41598-017-11542-0
call_split See protocol

[…] 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 to […]

library_books

Comprehensive classification of the PIN domain like superfamily

2017
Nucleic Acids Res
PMCID: 5499597
PMID: 28575517
DOI: 10.1093/nar/gkx494

[…] Structures of PIN-like domains superimposed in the previous step were compared to each other using DaliLite v3.3 () and GESAMT () from the CCP4 v6.5 package (). As a measure of their similarity, we tested Z-score returned by DaliLite and Q-score reported by GESAMT. The scaled scores were represente […]

library_books

Programmatic access to bioinformatics tools from EMBL EBI update: 2017

2017
Nucleic Acids Res
PMCID: 5570243
PMID: 28431173
DOI: 10.1093/nar/gkx273

[…] Workflow tools such as ps_scan (), InterProScan () and FingerPrintScan () have been retired, although some remain part of the InterProScan5 tool. ClustalW2 (), WU-Blast (), MaxSprout (), DaliLite (), DBClustal () and ReadSeq () have also been removed. […]

library_books

The evolution of function within the Nudix homology clan

2017
Proteins
PMCID: 5389931
PMID: 27936487
DOI: 10.1002/prot.25223

[…] nd edited using Jalview v2.8. For historical reasons, we first selected 46 out of 78 PDB structures and aligned them with five structural alignment programs: CE (version last modified July 16, 2008), DaliLite v3.1, MultiProt/STACCATO v1.0,, SSAP (accessed March 2008), and Structal (accessed March 2008). CE, DaliLite, and MultiProt/STACCATO were run locally. Alignments generated via SSAP and Struc […]

library_books

EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system

2016
PMCID: 4925161
PMID: 27130157
DOI: 10.1042/BCJ20160257

[…] of both EssC-N and EssC-C. 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 []. Crystal contact interfaces were analysed using PISA []. […]

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