After I got my model with basic modeling in MODELLER, a long 'hanging' strand with 31 amino acids was recognized. So I went to advanced modeling and remodeled my protein with multiple templates. I got my model and the problem was solved. Now, I encountered another problem about those loops in my model. There are 14 loops in my model, most of them are short loops but still, a few long loops are present in my model (i.e.loops with 13, 17, 19, 11, 9 amino acid residues). Should I do something on these loops? Are loop refinement are aim to optimize long loops?
I am confused about the advanced modeling and loop refinement in MODELLER. Are they perform for the same purpose, like modeling the unaligned sequence in the target protein? Or they have different purpose?
Please help me, I am really confusing now. Thank you!!!
Advance model building – Building a model with Multiple templates. Loop modeling – you need to define the loop regions of your predicted model. Its automatically refine and optimize the specified loop regions by building different loop conformation and compares it with all other conformations will give a estimate DOPE score. On basis of that you can choose the best-optimized loop.
@Vijayan Ramachandran Thank you for your answer!
So, if I do loop refinement in my model that modeled by Advance modeling, it should be alright right? And let say if I have 14 loops in my model, shall I optimize all 14 loops? Finally, do you know how to get the DOPE score? As in the tutorial, DOPE score output was absent, and I tried to get the output by using script:
m = MyLoop(env,
inimodel='BlTGH.B99990003.pdb',
sequence='BlTGH', assess_methods=(assess.DOPE, assess.GA341))
But DOPE score did not appear.
Thank you.
@Shaw Xian Au, If you want to run MD simulations for your systems, I do not see any need to struggle with loop protocols of MODELLER. These so-called advanced loop modeling methods are not very feasible in reality; only relaxing the amino acids.
In the case of long loops (>25) you should find some experimental data to help you model them properly.
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