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 < stephane.teletchea@univ-nantes.fr> 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/... > > 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 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >