Re: [modeller_usage] Modelling trans-membrane (TM) regions

Dear Stephane:

Many thanks for the suggestions. I did give a try to membrane-abinitio application in ROSETTA. It looks like probably I am doing some mistakes as all could get was a linear chain of amino-acids in the protein. I think this part is very poorly documented, and also most of the dependencies are so old that its tough to make it run properly.

Anyways, I have structures of three TM regions from a different approach and I was mainly looking for a way within MODELLER to assemble the whole structure. Indeed, I want to keep all three TM fragments in a plane. Would you suggest me some procedure (tutorial or some hints) to assemble the results (which was my original question) ?

Best,

Sushil

On Fri, Jun 24, 2016 at 6:43 AM, Stéphane Téletchéa <" target="_blank">> wrote:

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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