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Best scoring function ofr Structure Prediction

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Best scoring function ofr Structure Prediction

Hi everybody!
Any tip of a good scoring function for structure prediction? I want to do a first low resolution structure prediction from a sequence, using the centroid mode, but I don`t know which could be the best terms and the weight for each of them. In order to do it more complicated, the protein is a intrinsically unstructure protein, with some alpha helix content. Any tip?

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Thu, 2012-04-05 13:52

Dig into the ab initio application and see which scorefunction it's using.

The low-numbered scorefunctions available as weight sets (score0, score1, up through maybe score5?) are ported from Rosetta++'s ab initio. You can see their contents at rosetta_database/scoring/weights. I assume they're also used in Rosetta3's ab initio.

Generally centroid and fullatom scorefunctions have different terms - compare score4 (centroid) with score12 (fullatom standard) to see what I mean.

If you have a mostly unstructured protein, Rosetta is not going to be able to do much with it. There is a "REPLONLY" score function hack from Ray Wang in the Baker lab meant to allow unstructured regions to be repulsive-only. I have no idea if it's released or works in pyrosetta.

Thu, 2012-04-05 13:58