I'm headed in a similar direction. How big is your sequence? I'm planning to build some good old fashioned ball and stick or ball models of amino acids and then build peptide sequences of interest. Maybe come up with 22 simplified Lego like blocks for the modelling. I've seen the software for what you describe. Likely still really slow and its very hard to get 3D impressions well from a 2D display. I plan to go old school and avoid computers for my modelling. It'll likely be more informative and be faster than computer based modelling.
I came back to this post because I have a similar aim. I'm interested in the protein that strips ammonia from water. Ammonia removal is a big problem in water treatment. Ammonia and water a very similar chemically. As a result ammonia is hard to remove from water quickly or economically. We usually rely on microbes in a retention pond to do it slowly over many weeks or months. I've been hunting the protein and energy pathway microbes use to do this. I wrote the application highlighted in another post specifically to search these out from gene data. Now I intend to find some sequences for bacteria that remove ammonia and hunt for the mechanism.
I'm also interested in ion channels, ion pumps, etc. for similar water treatment application. I intend to find sequences for halophile bacteria which should be ripe with them and do similiar hunt for mechanisms.
