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Re: Regarding obtaining dimer form

Hi,
It is not clear to me from your question whether the template structure is actually in the dimeric form. Assuming it is, modeling a dimer is very easy with MODELLER. All you need to do is align the sequences of both monomers with the sequences of the corresponding monomers in the template structure. 

Your alignment would look like this:

>P1;template
structure:template:1:A:200:B:::::
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB*
>P1;target
sequence:::::::::
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX/YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
where the slash ('/') indicates the end of a chain. A, B are the two chains in the template. X, Y are the two copies of the target sequence.
You would use exactly the same procedure for a heterodimer. Since you have a homodimer you may also want to consider adding symmetry restraints during model building. For an example on this check the following list message: 


http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modeller_usage.archive.01/date/article-31.html

I hope this helps.

Best,

--
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
http://physbio.mssm.edu/~sanchez/




R Senthil Kumar wrote:


Dear modeller users,

 I am modelling a protein which is of homodimer in nature and this protein
matched with the same family protein which is also of homodimer.

 But matching with the only one chain(of two chains).So , i got a model in
a monomer form.How i have to use the modeller to get the replicate of
other monomer so my model will be of homodimer in nature.Please suggest me
ideas to overcome this problem.Thanks in advance.Expecting reply from your
people.

      ********************************
          R.Senthil kumar
          Junior Research Fellow(JRF),
          C/O Dr.Akash Ranjan,
          Computational & Functional Genomics(CFG),
          Centre for DNA Fingerprinting & Diagnostics(CDFD),
          ECIL road, Nacharam,
          Hyderabad - 500 076.
          India.

          E-mail:
Ph.no:040-7151344-EXTN(1304)--->Lab (2300)--->Hostel ********************************