Re: [IMP-users] can generate structure from sequences. how to add contact information as restrain?

[Ben Webb <>]

On 07/06/2012 10:36 AM, Adhikari, Badri (MU-Student) wrote:
> I am using edited version of
> http://www.salilab.org/~drussel/unstructured/imp_doc/atom_examples.html#structure_from_sequence
>  to generate structures from amino-acid sequences. This example uses
>  IMP.atom.CHARMMTopology.
>
> I would like to feed contact information as a restrain to guide the
> prediction process.

The script you are running is not really "predicting" 3D structures - 
they are generated purely from internal coordinates - so you'll always 
get extended chain structures (no secondary structure) with no 
consideration of excluded volume (clashes) or folding.

> 1.What should be the approach? Which classes/functions should be
> used?

You can use the extended chain structure as an input to an actual 
prediction, assuming you can express your contact information as one or 
more spatial restraints. Add stereochemistry, excluded volume, and your 
contact information restraints to the scoring function, and sample with 
the method of your choice (e.g. CG, MD, MC). There is a 
charmm_forcefield.py example which demonstrates the setup of the 
restraints, and there are several examples of optimizers.

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle