Re: [modeller_usage] Blast search for structures related to target
To: James Starlight <>, modeller_usage <>
Subject: Re: [modeller_usage] Blast search for structures related to target
From: Modeller Caretaker <>
Date: Wed, 16 Apr 2014 12:14:34 -0700
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.