Ruibin Liu
Ruibin Liu
Has anyone figured out how to solve the problem? I think 5J7S is problematic too.
It looks like `.apt/usr/bin:.apt/bin:.apt/sbin:.apt/usr/share:.apt/usr/lib` is appended to `PATH`. Shouldn't them all be like `/home/USERNAME/.apt/usr/bin`?
The missing residues are not matched, which is a caveat for some uses.
One difference in the comparison is that your Cython implementation only reads `ATOM`, `HETATM`, and `ENDMDL` lines while `biopandas` reads all. Would be interesting to compare the performance if all...
不支持Github issue
Okay, the test case is updated. I don't have access to the paper: http://dx.doi.org/10.1002/prot.340190207, so someone needs to finally verify it.
@peterjc Thanks for the paper! My understanding was partially correct that there should be 1 score for a sequence length of 9 but the current implementation has another problem. The...
I will take a look at the literature. If the method in the 1994 paper is still the best sequence-based flexibility predictor, I think we should keep it but still...
The Vihinen 1994 paper followed the same algorithm with Karplus 1985 paper which clearly used the three B_norm values (the Karplus paper had a figure showing the Fortran code). If...
According to the 1985 Karplus paper implementation, the neighbor-correlated B_norm values were only calculated for non-terminal residues, so the minimum sequence length when the window size is 9 is 11....