[modeller_usage] Protocol of modeling a membrane protein

[Qing Zhang <>]

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: 
Website: www.qingzhang.info
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