[BiO BB] Downloading PDB40D-B?

Theodore H.Smith delete at elfdata.com
Fri Dec 9 14:03:06 EST 2005

Hi people,

I am a researcher testing some new algorithms for protein and DNA  
searches for their performance in various areas. (Accuracy, time, RAM  

I'm reading that the protein database, PDB40D-B is useful for testing  
BLAST-like algorithms for their accuracy. http://www.pnas.org/cgi/ 

Is PDB40D-B actually a real database or must I construct it myself  
using self-made software out of other data?

I'm basically looking for a protein database to download, that I can  
test some BLAST-like software on. It doesn't need to be PDB40D-B,  
just any database that would allow for meaningful analysis of the  

Apparantly, PDB40D-B was "created" from SCOP, meaning that PDB40D-B  
isn't actually a downloadable database, it needs to be created  
yourself. Now I just need to figure out which files on SCOP's FTP  
section ( http://www.rcsb.org/pdb/cgi/ftpd.cgi/ ) I need to download  
and then figure out what to do with those files :)

Unless anyone else has a simpler suggestion?

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