Hi there,

I am currently writing a pipeline to identify distant homologs of genes in metagenomic samples using HMMER 3.0 and hmm models of conserved domains from Pfam.
Once I have identified putative homologs, I would like to verify that these homologs are indeed homologs by threading them onto a known protein structure and evaluating whether the threading was successful.
Given I'm very new to protein threading, is Modeller an ideal tool to use for this application? 

Many thanks,

Ben Temperton