Re: [modeller_usage] Blast search for structures related to target

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