Loop prediction

[Anonymous]

A protein is composed of N and C domains.
In the experiment, the protein was cut into these two domains and each of them was solved by crystallography.
However, the structure of the loop linking these two domains was unknown.
Therefore, I hope to predict the loop structure so that it can link the solved two domains.
How to achieve this goal?
Look forward to the reply.
Thanks.

[Anonymous]

The standard way is likely do do loop remodeling of that region. There are several protocols for this. (See https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/dc/d67/loopmodel_ccd.html https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/dd/d2d/loopmodel_kinematic.html and https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/db/dbe/next_generation__k_i_c.html Also take a look at the rosetta_demos directory (I believe it’s available as a separate download), specifically the model_missing_loop demo. The Meiler lab also has some published tutorials. Go to http://www.meilerlab.org/index.php/jobs/resources click on Rosetta Tutorials, then take a look at the “Homology or Loop Modelling”, and “Comparative Modeling, Loop Building and Clustering” tutorials. That hopefully should get you started.

There’s some additional protocols in the works for this sort of problem, but I don’t believe they’ve been published yet. (Keep an eye out for “Loop Hashing” from the Baker Lab, though it may be a while before that’s published.)

[Anonymous]

Yzhou,

You may also want to take a look at the Floppytail application to model the linker region:

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d8/d39/_floppy_tail.html

[Anonymous]

Thanks for your kind reply.
I will try these protocols.

[Author]

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