Hi,
I am trying to predict the structure of a protein using homology modelling. I sucessfully predicted the protein structure. But the template submitted in PDB is a monomer. The active protein is reported to be homo-dimer. So the predicted protein was a monomer. Are there any web-based servers for predicting the tertiary structure? I have a very minimal knowledge in programming. Kindly suggest me any steps to follow.
Thank you
Hello,
Do you actually have a PDB entry of the active homodimer of a similar protein?
If you do, you can construct your dimer using CHIMERA software. Can you give me more details of your work?
Regards
Hi Rodrigo,
Thanks for your reply.
The protein in PDB has homodimer as a biological assembly. However, when I was used Rosetta, only monomer was chosen as the template. Will there be any options in Rosetta (web interface only, as I am not good in programming or command interface) to select biological assembly as the template?
Hello Murthy,
Im not familiar with the Rosetta web server, but CHIMERA is free software and possess a great and easy to work graphical interface. You dont need to program anything.
You can download the program from here:
https://www.cgl.ucsf.edu/chimera/
Works in any operating system (Windows, Linux and Mac).
In this scenario I can help you for the construction of you homodimer.
Regards
Rodrigo
Hi Rodrigo
Thanks for the reply. I will try using CHIMERA.
Hi Sree
Using Modeller you can predict the structure of a putative dimer almost as easily as you can predict a monomeric structure. The question then becomes whether your putative dimer really exists. There may be something very obvious in the modelling that shows that it does not eg the presence of a big insertion which would disrupt the interface or, alternatively, a deletion that eliminates a large portion of it. Often, however, it's harder to tell. In that position I would compare the characteristics of your predicted interface with those of the known dimer. If the former produces similarly favourable scores to the latter then it suggests that your protein truly exists as a dimer. I would use PISA for this
http://www.ebi.ac.uk/pdbe/pisa/
or a newer version
http://www.ccp4.ac.uk/pisa/
Good luck
Dan
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