Single or multiple decoys from relax?

[Sally Ride]

I noticed that when refining the crude ab initio rosetta model with -relax and -nstruct higher than 1 the decoys you might obtain quite different structures (e.g. there might be quite significant changes in relative orientation of helices).

Is it common in the “official” rosetta ab initio protocols (for instance that used in CASP7) to generate multiple decoys with -relax starting from the same crude model? Or you rather generate single decoy from each crude ab initio model?

[Anonymous]

I think it is depends what you wanted to do with the generated structures. It might because the native model has big clash so that it causes the decoy to break down a lot. Generally, the more decoys are generated, the better coverage you will get.
If you want to keep the bond angles of native structure, you can try to use the flag -use_input_bond, which “Minimize or refold using the bond lengths and angles from the starting structure, useful for minimizing a structure without idealizing it first.”

> I noticed that when refining the crude ab initio rosetta model with -relax and -nstruct higher than 1 the decoys you might obtain quite different structures (e.g. there might be quite significant changes in relative orientation of helices).
>
> Is it common in the “official” rosetta ab initio protocols (for instance that used in CASP7) to generate multiple decoys with -relax starting from the same crude model? Or you rather generate single decoy from each crude ab initio model?
>

[Sally Ride]

> I think it is depends what you wanted to do with the generated structures.

Generally I would like to come as close to the general CASP7 ab initio rosetta protocol as possible. I cannot generate too many decoys with abrelax though so I am thinking about generating some tens of thousands decoys with standard ab initio and then running relax for cluster centroids and the some number of the lowest energy decoys from that clusters (generating single relaxed decoy for each initial crude decoy -nstruct 1). Then, I am going to do re-clustering of the relaxed structures to find the “best” decoys.

However, maybe it is better to select smaller number of starting crude decoys from standard ab initio mode for the next refinement stage and instead use the computational power to generate more decoys with -relax for each starting structure (that is -nstruct N). In other words I could discard some small and low energy clusters and instead generate more refined decoys from the “better” decoys from the first ab initio run.

>It might because the native model has big clash so that it causes the decoy to break down a lot.

Yes, it might be the case, I haven’t tested it thoroughly.

> Generally, the more decoys are generated, the better coverage you will get.

Of course, but I need to compromise this with my computational resources

> If you want to keep the bond angles of native structure, you can try to use the flag -use_input_bond, which “Minimize or refold using the bond lengths and angles from the starting structure, useful for minimizing a structure without idealizing it first.”

Ok, I will keep this in mind.

Cheers,
Janek

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