Blast search for structures related to target
Dear Modeler users!
I have a question about 1st part of basic modeller tutorial. As I understood the* profile.build() method could be useful for scanning *seq_database_file='pdb_95.pir' file where the sequences of the possible templates with known structures are provided against target which are defined further by means of aln.append(file='TvLDH.ali'). Does it possible to use blast search method within the modeller script to create such seq_database_file pir file firstly which will consist of all found pdb's structures with the defined threshold sequence against target sequence (e.g not less as 50% of sequence homology)?
Thanks for help,
James
On 4/16/14, 1:26 AM, James Starlight wrote: > Does it possible to use blast search method within the modeller > script to create such seq_database_file pir file firstly which will > consist of all found pdb's structures with the defined threshold > sequence against target sequence (e.g not less as 50% of sequence > homology)?
You can use any method you like to detect templates (for example, ModPipe employs PSI-BLAST as well as our own methods). You just have to ensure that the files you feed Modeller are in formats (e.g. PIR) that it understands.
Ben Webb, Modeller Caretaker
participants (2)
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James Starlight
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Modeller Caretaker