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Protocols

CaspR specifications

Information


Unique identifier OMICS_15387
Name CaspR
Interface Web user interface
Restrictions to use None
Input format FASTA
Output format PDB
Computer skills Basic
Stability No
Maintained No

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Publication for CaspR

CaspR citations

 (9)
library_books

Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8‐demethyl‐8‐amino‐d‐riboflavin to the antibiotic roseoflavin

2016
PMCID: 4982073
PMID: 26913589
DOI: 10.1111/febs.13690

[…] Initial attempts to solve the structure of RosA by molecular replacement were unsuccessful despite a thorough search for appropriate template structures using the online tools phyre2 , fugue and caspr . Therefore, RosA labelled with selenomethionine (SeMet) (seven methionine residues in 353 amino acids) was produced, and the structure was solved by multiple‐wavelength anomalous dispersion (MA […]

library_books

Clinical relevance of positive voltage gated potassium channel (VGKC) complex antibodies: experience from a tertiary referral centre

2013
PMCID: 4451115
PMID: 23757422
DOI: 10.1136/jnnp-2013-305218

[…] Serum VGKC-complex antibodies were tested using a radioimmunprecipitation assay. Cell-based assays for CASPR2, LGI1 and contactin 2 antibodies were performed using human embryonic kidney cells transfected with cDNAs encoding the relevant proteins. […]

call_split

A Novel N Acetylglutamate Synthase Architecture Revealed by the Crystal Structure of the Bifunctional Enzyme from Maricaulis maris

2011
PLoS One
PMCID: 3236213
PMID: 22174908
DOI: 10.1371/journal.pone.0028825
call_split See protocol

[…] ructural refinement greatly improved when additional restraints from known homologous structures were introduced .The structure of the hexagonal form of xcNAGS/K was solved in space group P6222 using CaspR, the web-server for automatic molecular replacement and the structure of mmNAGS/K as the search model. The solution from molecular replacement is consistent with the electron density map constr […]

library_books

Current methods in structural proteomics and its applications in biological sciences

2011
3 Biotech
PMCID: 3376864
DOI: 10.1007/s13205-011-0037-1

[…] kov ), AMoRe(Navaza ) and Phaser(McCoy et al. ). To further streamline the MR procedure, a number of automated MR pipelines have been developed. These include the Bias Removal Server (Reddy et al. ), CaspR(Claude et al. ), BRUTEPTF(Strokopytov et al. ) and MR pipeline (Schwarzenbacher et al. ). Other developments include Auto-Rickshaw(Panjikar et al. ) which is principally used for experimental ph […]

library_books

Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

2011
PLoS Genet
PMCID: 3116920
PMID: 21698144
DOI: 10.1371/journal.pgen.1002117

[…] ture was carried out using COOT version 0.5 and REFMAC in the CCP4 suite . The root mean square deviation (RMSD), a measure of the overall similarity between protein backbones, was calculated using CaspR . Interpretation was focused on Chain B, which displayed lower overall b-factors and had fewer crystal-packing contacts. Coordinates have been deposited in PDB with accession 3RY9. […]

call_split

The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold

2011
PLoS One
PMCID: 3073944
PMID: 21494601
DOI: 10.1371/journal.pone.0018528
call_split See protocol

[…] using the Phenix software including manual rebuilding and rigid body refinement followed by several cycles of positional refinement.For the second crystal form, we used molecular replacement on the CaspR server and the MAD-solved three-dimensional structure of CA3427 as template. The structure was refined using COOT and iterative steps of manual rebuilding and positional refinement using Phenix […]

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CaspR institution(s)
Information Génomique & Structurale (UPR CNRS 2589), Institut de Biologie Structurale et Microbiologie, Marseille, France

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