[BiO BB] PISCES inconsistencies

Semen Esilevsky yesint4 at yahoo.com
Mon Mar 27 05:04:13 EST 2006

> It would be useful if you could describe the
> problems you are 
> having with PISCES, as that is a very popular and
> commonly used database.

Ok here is what I've found in the databases of the
stand-alone PISCES package. Probably this information
will be useful for somebody else.
1) The FASTA file pdbaa and the alignment file
pdbaa.align are not consistent. There are (very few)
entries in pdbaa.align, which are absent in pdbaa. 
2) As far as I understand pdbaa.align should contain
two entries for each pair: aaaa vs bbbb and bbbb vs
aaaa. For few proteins only one of them is present.
Many pairs are simply missed with no explanation (I
suspect that I just misunderstand something at this
point, however).
3) There are some formatting errors in pdbaa.


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