Hi everyone,

Is it possible to perform an automatic search of a multi-chain PDB template with a known protein sequence that is to be modeled (say 100-200 residues in length) and then extract the chain ID of the segment of the PDB template that best matches with the query sequence.

As far as I understand, if you align a protein sequence against a multi-chain PDB template in MODELLER, it generates an alignment file (PIR/PAP) that does not automatically give you the chain ID of the PDB segment against which the alignment has been performed. Of course, this is a non-issue if you work manually but I would like to automate modeling for a large number of sequences.

Any insights would be greatly appreciated.

Thank you! Amjad

*************************************************************************************************************************************************** *AMJAD FAROOQ PhD DIC | Associate Professor* Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net ***************************************************************************************************************************************************