I would like to try your membrane ab-initio modeling protocol of rosetta, to model a membrane protein of 6 TM regions. But I am not sure how your protocol should perform compared to homology modeling, this protein has 370 aa and has a distant template of about 20% id for 300 aa region. I wonder if rosetta ab-initio method could produce equivalent or better results than the comparative modeling based on the template we have, and what is the best course to follow. And wether or not the results will be comparable.
Best regards and thanks a lot,
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion – Israel Institute of Technology
Haifa 32000, ISRAEL