Hello I am trying to use SWISS-MODEL to draw 3D model for SDCCAG8 protein. My problem is that resulted templates and models do not cover the entire protein sequence properly and a big part of my protein sequence is not involved in modeling. I have the same problem in modeling with CSF1R protein. Anybody knows the solution for this problem? I will be so pleased if you could share it with me.
SWISS-MODEL does comparative modeling (AKA template modeling). It can model - poorly - a part of your protein that is lacking a template in the middle, but it can't model the portion at either end without a template. Here is a diagram:
SDCCAG8 AAAAAAAHHHHHHGGGGGGGDDDDDDDD template AAAAAAA------GGGGGGG--------
SWISS-MODEL will model the HHH portion of your protein because it is anchored at both ends by a matching template, but that HHH section won't be worth much because it is unlikely to be very accurate. The DDD portion of your protein will not be modeled at all since it does not have an anchor at its C-terminus. You can probably force it to model the DDD part, but it will be fairly useless if longer than 10-15 residues. In other words, it is better to have a reliable partial model of your protein than to have a complete model for which parts are very likely to be meaningless.