Hello,
I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?
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Hello,
I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?
https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/HybridizeMover
https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/abinitio-relax
https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file
Hi, smlewis. Thanks for your reply.
I found that HybridizeMover requires a template. But I have no template for builting model.
I have tried to use abinitio-relax for structural prediction and added experimental constraint as follows:
AtomPair CB 63 CA 65 FLAT_HARMONIC 3.47 1.0 0.50
AtomPair CB 67 CB 69 FLAT_HARMONIC 6.47 1.0 0.50
....
Dihedral C 3 N 4 CA 4 C 4 CIRCULARHARMONIC 1.71 0.50
Dihedral N 4 CA 4 C 4 N 5 CIRCULARHARMONIC -2.33 0.50
Dihedral C 4 N 5 CA 5 C 5 CIRCULARHARMONIC -1.72 0.50
....
But the result is very different from the naive structure. I'm wondering what went wrong.
Any help would be appreciated.
There are a thousand places this could go wrong. I don't actually know what is wrong - particularly I cannot parse "the result is very different from the naive structure". If you mean naive as constraint-free: I would expect that the constrained result should be very different, that's the point of constraints. If you meant 'native', then I don't know why you don't have a template for hybridize.
If you are doing effectively ab initio with constraints, I would guess the constraints aren't strong enough during the early stages; perhaps they are not on at all if they are not active in the scorefunction. I can guess another dozen things that might be wrong but I don't have enough data to tell.
You should probably re-ask this in a new thread; it's easier to get attention to unanswered posts and I clearly don't know enough about what you are trying to do to help.
We have increased the weight of the constraint and this problem is solved.
Thank you very much!