To generate a total of 100 decoy sets, MODELLER was used with the selected template structure.
PRALINE [ 23] at http://www.ibi.vu.nl/programs/pralinewww/ was used to align the BauA and the selected template, that is, FptA sequences.
Multiple alignment of the protein of interest and the selected template sequences were executed using ClustalW [39].
Furthermore, simulation results show that using a randomly selected template consistently gave superior results to those achieved using templates from the fittest parent or grandparent.
In addition, the memory overhead for all five doctors was around 236.2, 47.2, and 73.2 MB for using all templates, selected template representatives, and compressed template representatives, respectively.
Homology model of LPKC using crystal structure of selected templates was built using multi-template protocol of MODELLER version 9.10 [ 28, 29].
Second, relative to using all of the original templates as discussed in Section 5.3.2, using 20% template representatives that were selected by MLTS with the KL distance slightly decreased phone accuracy by 0.21% (from 74.26% to 74.05%), but using the template representatives selected by MDTS with the LLR distance significantly decreased phone accuracy by 0.69% (from 74.51% to 73.82%).
These homologs are used to select templates for homology modeling.
Fold-recognition alignments to the structures of selected templates were used as a starting point for homology modeling using the "FRankenstein's Monster" approach [ 34], comprising cycles of model building, evaluation, realignment in poorly scored regions and merging of best scoring fragments.
Briefly, fold-recognition alignments to the structures of selected templates were used as a starting point for homology modeling using the "FRankenstein's Monster" approach [ 82], comprising cycles of model building, evaluation, realignment in poorly scored regions and merging of best scoring fragments.
