Dear all,
I have generated a database of protein sequences and selected a few sequences from it based on some criteria. Now i would like to model these selected sequences and see if they folded into the native structure of a protein. The protein (native) shares a sequence similarity of 40% with all the sequences in the database.
As i- tasser uses NR database from pdb to generate sequence profile for the target sequence,will it be theoretically correct to use a locally created database of proteins instead of NR database.
Hope i am able to make myself clear. Please ask for more clarity if required and suggest if the idea is feasible .Thanks in advance.
Yes you can use your own database of sequences but the question arises why you want to use your own database? Using NR database will provide a better profile rather than using your own database. Moreover if you want to perform some benchmarking where you want to define some cutoff for sequence identity then this feature is also available in I-TASSER using " -idcut " argument.
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