Dear Modeller users:

I just started using Modeller (version 8v1) and would like to find a good protocol of modeling membrane proteins that contain helices, beta-sheets, loops, and long N and C-terminal tails. By reading Modeller manual and some papers, I have a rough plan like this:

1. Find the closest sequences in PDB using Blast [done].

2. Do sequence alignment with the best PDB structure using ClustalW [done with a score of only 15]

3. Build 10 models in Modeller with 3 repeats of very thorough VTFM optimization and MD optimization until max_molpdf <= 1E6 [done]

4. Pick the best model based on the quality of helices and beta-sheets only since loops have not been very optimized [I do not know much about verifying protein structure quality; it seems WHAT_CHECK is a good program to use; any suggestions?]

5. Optimize loops in Modeller for the above best model and obtain several loop models

6. Pick the best loop model with quality check

7. Molecular dynamics simulations?

Any suggestions on this? Thanks in advance.

Sincerely,

Qing

====================================== Qing Zhang, Ph.D. Research Associate Department of Molecular Biology, MB-5 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000 Tel: (858) 784-2333 Fax: (858) 784-2860 Cell: (917) 509-3182 Email: qzhang@scripps.edu Website: www.qingzhang.info ======================================