[BiO BB] How to find the same proteins?

Semen Esilevsky yesint4 at yahoo.com
Thu Mar 23 04:30:58 EST 2006

Dear all,
I'm a novice in bioinformatics and this question is
probably stupid, but...
I have a list of ~200 PDB id's. For each of them I
have to build a list of all entries in PDB, which
represent the same protein (say, >99% sequence
similarity and no large gaps). Could someone suggest
me the least painfull way of doing this?
As far as I understand all what I need is the database
where all pairwice BLAST allignments of PDB chains are
stored. I've found one as a part of a PISCES server,
but it is incomplete and contains some internal
inconsistensies. Could someone suggest me a better one
or there is a simpler way out?


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