I am modeling my protein with MODELLER, and I referred to both MODELLER official site and youtube for the process. From MODELLER site, the structure used for template selection are generated in the build_profile.pir file. While in youtube, the structure sequences used for template selection are taken from BLAST. The outcome for these two method are different. Anyone know what has caused this to be happened? Is that due to the alignment algorithms used in both workspace?
Thank you.
The basic difference is that when your run BLAST you search sequences similar to yours over the "entire" database while the algorithms implemented in most homology modeling servers search over a "subset" of sequences whose structure is known. Typically the search is restrained to the PDB. Take a look at:
http://www.cmbi.ru.nl/edu/bioinf4/articles/homologymodeling.pdf
I'll recommend u must do blast. Everyday new sequences and structures are updated in database. So if you'll take blast result then u'll get the most recent result. But if you're going to take modeller selected results then probably u'll miss the recent one. Because modeller is a standalone software which is installed in your pc and it's containing the old database.
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