On 1/19/10 1:34 PM, Ben Temperton wrote: > 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? You could probably use it, but I don't know if it would be the best tool for the job. Given an alignment between a known structure and a sequence, Modeller will always build a model. You could certainly use an assessment score such as normalized DOPE to estimate whether the model is a good one, but I'm not sure where you'd pick your cutoff - it would be something for you to tinker with. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage