de novo protein prediction

[Anonymous]

Dear Rosetta Users

I’m recently studying the Rosetta de novo folding method.

All tutorials for Ab initio structure prediction in Rosetta overview was evaluated by total score vs rmsd between predicted model and native structure.

My question is

if there is no native structure. How can I evaluate and select the best structure in predicted structures.

Thank you in advances

[Anonymous]

I don’t have experience with ab-initio but here’s my understanding:

When no native structure is available  you just use the lowest scoring structure as a surrogate for the  native structure when building your plot. 

The “funnel” shape is really only intended to demonstrate that favorable scoring models tend to adopt a similar pose. Due to this fact an arbitrary low scoring model to demonstrate this (lowest is typically chosen by convention).

I went and grabbed a couple of resources to confirm my understanding:

The ab-initio tutorial here confirmed the thing about using the lowest scoring model as a surrogate for the native structure: http://www.meilerlab.org/index.php/rosetta-tutorials

Paragraph 2 of this discusses the importance of the funnel shape in a score vs rmsd plot: https://new.rosettacommons.org/docs/latest/getting_started/Analyzing-Results

[Anonymous]

hello taylorjones. thank you for a quick response. the information that you provided helped me understand the analyses of ab initio prediction results. according to your oppinion, i’ll study and try it . thank you 

[Author]

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