deconSTRUCT protocols

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deconSTRUCT specifications

Information


Unique identifier OMICS_03654
Name deconSTRUCT
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Iva Mihalek <>

Publication for deconSTRUCT

deconSTRUCT in pipeline

2017
PMCID: 5372573
PMID: 28273846
DOI: 10.3390/ijms18030557

[…] using ramachandran plots [] obtained from procheck [], prosa [], qmean [] and errat []., secondary structure elements and the structure topology of cstegu20.6 were analyzed using profunc []. the deconstruct [] and dali [] were employed to detect the aligned regions of proteins based on structural similarities. the oligomeric state of the structure was predicted using galaxygemini [], […]


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deconSTRUCT in publications

 (4)
PMCID: 5469503
PMID: 28570695
DOI: 10.1371/journal.ppat.1006394

[…] of data collection and refinement statistics are given in . search for structural homologs of sidk (16–278) was performed with the dali server [], pdbefold [] (http://www.ebi.ac.uk/msd-srv/ssm), and deconstruct []., * friedel pairs counted as independent reflections., v-atpase and v1 were purified from s. cerevisiae as described previously [] via a c-terminal 3×flag tag on the a-subunit. […]

PMCID: 5372573
PMID: 28273846
DOI: 10.3390/ijms18030557

[…] was confidently folded, and the 3d cartoon of the model was colored by the per-residue error according to the b-factor values ()., the results of the structure-based search for homologues using deconstruct [] showed that cstegu20.6 has the highest homology with several dlcs, followed by ribosomal proteins and calcium-binding proteins (). we superposed the structures of two dlcs (pdb ids: […]

PMCID: 3582452
PMID: 23445440
DOI: 10.1186/1471-2164-14-S2-S1

[…] r is an introduced parameter of small values., many different approaches for protein structure comparison apply the secondary structure elements (sses) representation and database searching, such as deconstruct [], ssm [], gangsta [], mass [,], vast [], tops [] and approaches in [-]. our approach epc utilizes the sse-based representation of the protein structure, and takes into consideration […]

PMCID: 3430279
PMID: 22942748
DOI: 10.3390/ijms13078998

[…] alignment suggests a close proximity between brbv and fmdv 3dpol followed by hrv-16 and rhdv 3dpol., the modeled structures of brbv 3dpol prepared by geno3d and swiss-model [–] were submitted to the deconstruct web server. dconstruct finds homologous proteins via a totally different approach as discussed in the materials and methods section []. the details of the modeling protocol and analysis […]


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deconSTRUCT institution(s)
Bioinformatics Institute,Matrix, Singapore

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