I'm studying a transmembrane ion channel (protein 1). There are structures of protein 1 in a closed conformation, and I am interested in the open conformation. There is a very similar protein in an open conformation (protein 2). So I am trying to thread the sequence of protein 1 onto the atomic model of protein 2. I know the template.
I tried robetta and swiss prot for this. How should I do things with modeller? Could someone point me to a tutorial? The sequences are quite similar, except for some insertions. I know my protein very well and am looking for a protein modelling approach where I can have low level control, and manual manipulation at the sequence alignment and structure level. I don't need something that does everything automagically.
-- Geoffrey Woollard, MSc PhD student Department of Medical Biophysics, University of Toronto Princess Margaret Cancer Centre, University Health Network