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Homology modeling using the automated mode of SWISS-MODEL (http://swissmodel.expasy.org/, last accessed June 16 , 2014 was performed (Kiefer et al. 2009).
The tertiary structure of rhizobial Glbs was modeled using the automated mode of the I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/), which also provided the best structural homologs to the query sequences.
Structures of endo-1,3-β-glucanase from Cellulosimicrobium cellulans (PDB ID: 3atgA) and the C-terminal Ig-like domain of the bacteriophage λ tail tube protein (PDB ID: 2l04A) were used as templates for protein structure homology modeling using the automated mode of SWISS-MODEL [ 22].
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For 3-D modelling of proteins the SWISS-MODEL server (http://swissmodel.expasy.org/workspace/) at the Swiss Institute of Bioinformatics (SIB) was used in the automated mode [107], [108].
After minimum 1 h incubation, the absorbance was measured at 490 nm using the automated Cytation™ 3 Cell Imaging Multi-Mode Reader (Biotek, Winooski, VT, USA).
Parameters computed using the automated method were consistent with the parameters computed using the non-automated method.
Central subfield thickness (CST) was measured using the automated software.
Transcripts were counted using the automated NanoString nCounter® system.
Blood cultures were processed using the automated blood culture system.
Some sites using the "automated" method can incorporate this.
Modelling was carried out by the automated mode and also using a specified structure entry from the protein data bank (PDB) as template.
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