Which score4?

[Anonymous]

Hello everybody.

I read that the final step in the low-resolution part of a rosetta classic ab-initio protein fold prediction protol should be rescoring the obteined structures with the score4 in order to discriminate the native-like structures.

Looking for this score4 I could find the following score4-like scores (both in the pyrosetta package and rosetta3.4 package): “score4L”, score4_smooth”, score4_smooth_cart”.
In all papers I’ve read I could not find any references to any of them but only to “score4”. Does anybody know which this “score4” is?

Thanks in advance

[Anonymous]

For ab-initio, you should be relaxing the resulting structures after abinitio in a full-atom scorefunction (score12). Then you want to cluster the structures + rescore them using the full-atom scorefunction, if you don’t have the scores from the relax step. For clustering, I would recommend calibur. Its quick and easy http://sourceforge.net/projects/calibur/

In the C++ application, this is known as Ab-Relax. To do this in PyRosetta, create + run a fastrelax instance after you bring the model to all-atom + repack:

rel = FastRelax(scorefxn)
rel.apply(pose)

Hope this helps

[Anonymous]

You want score4L. score4L is 5 years old and is thus related to the original algorithm…the others are newer and are used for variants other than classic ab initio.

[Anonymous]

oh! i just realized the score4L is a patch file……which score is it meant to be added to? anybody knows?

[Anonymous]

grepping the codebase strongly suggests cen_std.

cen_std:
env 1.0
pair 1.0
cbeta 1.0
vdw 1.0

score4L:
hbond_lr_bb = 1.0
hbond_sr_bb = 1.0
rama = 0.1
chainbreak = 1.0
rg = 2.0

There is basically no overlap between these term sets, so they’ll place nicely.

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