Hi,
I have a list of pdb structures for which I have to find the fold and class. I used the parseable files from SCOP ftp and used it through a perl script. But, later I found that many structure entries are missing in SCOP database. Then I tried to use the CATH database, but it seems it too have some missing pdb entries. So, I want know in such a situation , how can I manually do the class and fold classification for my dataset. Please help in this regard
BHARAT
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bharat.85.monu •
1 answer
An option which crosses my mind is to do the blast search of your chains (pdb entries) agains the already annotated entries. In case you got a reasonably high hit you have a new annotation. To my knowledge CATH has a slightly bigger pdb database coverage, so I would use it as a reference.
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Would help to provide an example or two of PDB codes that you believe are missing from SCOP/CATH.
3os4, 4eqp, 4ebg.....
If such pdb are not in the databases (cath/scop), maybe you could follow their protocols to assign their classification. You should find the protocols in their papers.