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3D-Blast specifications

Information


Unique identifier OMICS_03684
Name 3D-Blast
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for 3D-Blast

3D-Blast in publications

 (8)
PMCID: 5767921
PMID: 29379263
DOI: 10.6026/97320630013430

[…] to identify the pharmacophore, the modelled structure was used as a query to search for possible pdb structures having a bound substrate or substrate analogue. this search was performed using 3d-blast. the substrate analogue, d-xylitol which is cocrystallized in 4gna (mouse smp30/gnl-xylitol complex []), was docked onto the model to understand the residue level conservation […]

PMCID: 4280198
PMID: 25549250
DOI: 10.1371/journal.pone.0115020

[…] the validated protein model structures of good quality obtained through modbase, phyre2, and i-tasser along with the associated target structures identified by psipred and fugue were submitted to 3d-blast for scop classification which searches for the longest common substructure called sahsps (structural alphabet high-scoring segment pair). this is a fast and accurate method for discovering […]

PMCID: 3521469
PMID: 23281852
DOI: 10.1186/1471-2164-13-S7-S21

[…] peptide segments (i.e. pharma-motifs), which surround the ligand-binding site. by transforming the 3d structure segments into 1d structural alphabet sequences through in-house tool (called 3d-blast [,]), we can rapidly search the potential target proteins with similar binding environment against protein data bank (pdb) []. and then a structural alignment tool, such as dali [], was used […]

PMCID: 3423939
PMID: 22928109
DOI: 10.1155/2012/976385

[…] or their transformed representations was necessary for other structural studies predicting also functional interaction sites. the corresponding research yielded two servers with different 3d-blast programs enabling us to compare folds and fold families [, ] (for details see also ). alternative structural comparison substituting 3d relationships was performed when searching […]

PMCID: 3205055
PMID: 22073123
DOI: 10.1371/journal.pone.0027044

[…] been compared with the corresponding models obtained through modpipe workflow by excluding the crystal structures in the template search step. folds of all the proteins were also obtained through 3d blast and all the models indeed have the correct fold as that of the corresponding crystal structure, with an average rmsd of about 2 å (), indicating high levels of confidence in the methodology […]


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3D-Blast institution(s)
INRIA Nancy - Grand Est, LORIA, Vandoeuvre-lès-Nancy, France

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