Le 23/06/2016 à 06:24, Sushil Mishra a écrit :

Dear all:

I am quite new to MODELLER and I would like to know if it is possible to to models a protein having with few trans-membrane (TM) regions. Are there such an example or tutorial available? I tried to search archive but, unfortunately, there was nothing that can help me. Is it possible to assign a few TM regions (in the form of restrain or something like that) which would be modeled in a plane. Any suggestions/inputs related to modelling enzyme having TM regions will be appreciated. My system has very poor similarity (< 20 %) in PDB, and also no similarity between TM regions of query and TM regions of proteins in PDB.

Best,
SK

Dear Sushil,

Membrane protein prediction is the most difficult modelling part you'll have to address.
If possible, decompose your protein into different domains and assemble them adterwards.

For the transmembrane region, since mostly no templates are available, I would recommend using
ROSETTA for this purpose and MODELLER to assemble the results, but not MODELLER alone, see for instance:
https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/db/d38/membrane_abinitio.html

You could also have a look at
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556676/
and
http://opm.phar.umich.edu/
and certainly:
http://www.dsimb.inserm.fr/dsimb_tools/anvil/
http://www.dsimb.inserm.fr/dsimb_tools/maiden/

Best,

Stéphane

--
Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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