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Protocols

iPBA specifications

Information


Unique identifier OMICS_03747
Name iPBA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for iPBA

iPBA citations

 (6)
library_books

Fungal Screening on Olive Oil for Extracellular Triacylglycerol Lipases: Selection of a Trichoderma harzianum Strain and Genome Wide Search for the Genes

2018
Genes
PMCID: 5852558
PMID: 29370083
DOI: 10.3390/genes9020062

[…] rs short chain-TAG but retains 20% of relative activity on long chain C18:1 TAG []. CHSQG pentapeptide has not been identified in any characterized lipase so far. Three-dimensional superposition with IPBA software of each T. harzianum lipase model with its respective best template model permitted the identification of putative lid domain, catalytic triad, the pentapeptide sequence and the oxyanion […]

library_books

An Insight Into Structure, Function, and Expression Analysis of 3 Hydroxy 3 Methylglutaryl CoA Reductase of Cymbopogon winterianus

2017
Bioinform Biol Insights
PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] The ProSA tool was used to assess the energy profile of the CwHMGR model. The root mean square deviation (RMSD) of the corresponding Cα-atom pairs of both the model and template was calculated using iPBA Web server. Finally, the refined model was subjected for further refinement by molecular dynamics (MD) simulations. […]

library_books

The structure of Erb1 Ytm1 complex reveals the functional importance of a high affinity binding between two β propellers during the assembly of large ribosomal subunits in eukaryotes

2015
Nucleic Acids Res
PMCID: 4678814
PMID: 26476442
DOI: 10.1093/nar/gkv1043

[…] Dali Server and iPBA server were used for similarity searches in the PDB (,). Sequence multi-alignments were done with JalView (). Dimer stability and assembly analysis were performed by PISA server (). Structure rep […]

library_books

Molecular cloning and in silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765

2014
BMC Res Notes
PMCID: 4209082
PMID: 25304397
DOI: 10.1186/1756-0500-7-713

[…] qmean/cgi/index.cgi) []. On the basis of model stability, best model was selected from SWISS-MODEL server. The PyMOL (http://www.pymol.org/) [] software was used to visualize the 3D structure and the iPBA webserver (http://www.dsimb.inserm.fr/dsimb_tools/ipba/) [] was used for superimposing the generated model with its template model. […]

library_books

PMCA4 (ATP2B4) Mutation in Familial Spastic Paraplegia

2014
PLoS One
PMCID: 4132067
PMID: 25119969
DOI: 10.1371/journal.pone.0104790

[…] cture . The uncharged residue (Glutamine, Q) in mutant protein has a different configuration from the positively charged residue (Arginine, R) in wild-type protein (). Structure alignment analysis by iPBA found 3 local differences in the 3D structure between wild-type and mutant proteins [ (i–ii)], which may affect protein function . […]

call_split

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

2012
PLoS One
PMCID: 3382195
PMID: 22745680
DOI: 10.1371/journal.pone.0038805
call_split See protocol

[…] of local structures in proteins with an average root mean square deviation (rmsd) of 0.42 Å . The assignment of PBs has been carried out using an in-house Python software similar to the one used in iPBA web server . highlights the correspondence between PBs and regular secondary structures assigned by DSSP (Dictionary of Secondary Structure of Proteins) . The PBs m and d are prototypes for the c […]

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iPBA institution(s)
INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Université Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, Paris, France

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