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.