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jgreener64 / ProteinEnsembles.jl

Generate and perturb protein structural ensembles using the ExProSE algorithm
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User specified constraints #2

Closed ssrb19 closed 6 years ago

ssrb19 commented 6 years ago

Hello,

I was wondering if the user can specify CA constraints. Say I have two proteins and I know that residues x of protein A interacts with residue y of protein B. Is it possible to get perturbations of protein A that satisfy this constraint?

Thanks.

jgreener64 commented 6 years ago

It's not possible to do this easily. You can alter the interaction matrix manually to change the relevant entry to a bond, e.g. add

inters[n1,n2] = 1
inters[n2,n1] = 1

after line 702 of src/interactions.jl, or modified versions after lines 722 and 728 if you are using two conformations. n1 and n2 should be the exact indices of the atoms to be constrained. I'm not sure a single constraint will be enough to affect the system significantly though.

ssrb19 commented 6 years ago

Thanks for the prompt response. I can try doing that. Is there a way of giving more weights to certain interactions? If I could up-weight these few interactions significantly, it might affect the system at large.

jgreener64 commented 6 years ago

There is not currently a way to up-weight certain interactions - at the moment they are sampled uniformly. Either you could change the sampling (lines 50-54 in src/generate.jl) or just add the same constraint multiple times when creating the Constraint object, so that it is chosen more often.