Increase compactness of decoys

[Sally Ride]

What are the ways to increase the compactness of decoys in rosetta standard ab initio mode?

Are the -vdw_reweight and -rg_reweight (and maybe -cb_reweight) the right options to choose? Or they change only the final scoring rather than influence the simulation?

[Ora Furman]

Do you mean you want to increase the packing of the protein?Is there a sasapack score in the outputs?
What is the average number?

> What are the ways to increase the compactness of decoys in rosetta standard ab initio mode?
>
> Are the -vdw_reweight and -rg_reweight (and maybe -cb_reweight) the right options to choose? Or they change only the final scoring rather than influence the simulation?
>
>

[Sally Ride]

I mean rather decreasing the radius of gyration.

I am folding a structure containing six helices. It folds into two three-helix-bundle units which, however, in most decoys do not interact closely with each other. In other words in most decoys the two helical units do not form common hydrophobic core.

I would like to try to force rosetta to generate higher fraction of “compact” structures.

Regarding the scores: for some random set I have averages:

sasapack 1.57

rg 17.13

After changing -rg_reweight to 2.0:

sasapack 1.63

rg 16.7

And -vdw_reweight 2.0:

sasapack 1.82

rg 17.16

so virtually there is no difference. What else I could do?

> Do you mean you want to increase the packing of the protein?Is there a sasapack score in the outputs?
> What is the average number?
>

[Anonymous]

Could you try to use the constraints file to restrict the movements?

> What are the ways to increase the compactness of decoys in rosetta standard ab initio mode?
>
> Are the -vdw_reweight and -rg_reweight (and maybe -cb_reweight) the right options to choose? Or they change only the final scoring rather than influence the simulation?
>
>

[Sally Ride]

Indeed, probably the constraints will be my next move if I fail with the standard approaches. At first I would like to get maximum from less biased rosetta runs though and maybe if the energy function drove structures to more compact states the representation of well folded structures could be much higher (at least that is what I hope).

Anybody knows whether -vdw_reweight, -rg_reweight and -cb_reweight options should affect the folding simulations?

> Could you try to use the constraints file to restrict the movements?
>
> > What are the ways to increase the compactness of decoys in rosetta standard ab initio mode?
> >
> > Are the -vdw_reweight and -rg_reweight (and maybe -cb_reweight) the right options to choose? Or they change only the final scoring rather than influence the simulation?
> >
> >

[Sally Ride]

I have got the response from rosetta support that indeed the flags modify the energy function during the whole modeling procedure

> Anybody knows whether -vdw_reweight, -rg_reweight and -cb_reweight options should affect the folding simulations?

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