Forwarding to list.
From: Denis Volkov D.Volkov@artcustoms.ru Subject: Fwd: Re: model_refinement
===8<==============Original message text=============== Hi, Oliver! First of all thank you for your help! I'll try to run Procheck on every template. As to alignment...automatic alignment produced by Modeller and ClustalW didn't satisfied me. The problem is that I'll try to model unknown retroviral aspartic protease and all enzymes of this class share a little similarity. So I used manually adjusted alignment based on knowledge of conserved regions of this class. No, I didn't used any restrains during all MD steps. I thought that this is a little bit unnatural to fix one region and don't other. But now I think that this may be a clue. But I have another question: If I've got so little similarity can I used a data of predicted secondary structure(I know that Modeller can do it)? Will it improve a quality of a model?
Thanks in advance
Denis Volkov Enzyme Laboratory,IBCH RAS