Drear members,
I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.?
I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here?
Many thanks in advance
Regards Anu
On 11/10/2014 12:20 AM, aneesh cna wrote: > I am a new comer to modeller. I am trying to model a ~15AA long missing > loop region in a homo-dimer. Both monomer units in the homo-dimer > missing the loop region. Unfortunately, my template is a monomer unit. > How can I model the loop region in both monomer together.?
Modeling the two loops is simple - just select both regions in select_loop_atoms() as shown at http://salilab.org/modeller/9.14/manual/node36.html But 30 residues is really long - you'll need to build a lot of models to hope to reasonably sample conformations.
Actually building the comparative model of a dimer from a monomer template is a different story, but this is already discussed at http://salilab.org/modeller/9.14/manual/node29.html
Ben Webb, Modeller Caretaker
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aneesh cna -
Modeller Caretaker