[BiO BB] how pdb ID is defined?

[Mike Marchywka]

> You may use sequence alignment tools (e.g. ClustalW) to determine the
> biological distance between your interested proteins, or use "Sequence
> Search (http://www.rcsb.org/pdb/search/searchSequence.do)" provided by RCSB
> PDB to find similar proteins, actually, it is a BLAST service.

I actually "discovered" the redundancy in the entries by accident trying to make a 3D
lookup tool. So, I have a couple of comments. 

1) Are there 3D lookup databases? I think this came up earlier but I'm not sure anyone
completely answered although we discussed 3D alignment tools for given entries, I'm not
sure you could make a 3D query.

2) I've gotten a ( non-useful ) tool to work on a "database" of a few hundred pdb files.
In fact, the tool could accept a query and find exact 3D matches ( rotationally invariant )  but it
was awful at finding "similar" things- I got lots of hits but noted all the names
were similar as per the earlier comments. I stopped at this point and went back to various topics like
mechanical CAD literature to see if I could improve the approach.
I have some examples posted here ( and you will note that
I have placeholder/failures up there right now but don't intend to fix right away):

http://www.spottext.com/marchywka/glutp/docs_surfaces.html?src=biolist

If anyone has links to papers on surface descption algorithms they may be helpful in
refining the approach.  The surface FINDER looks ok as it seems to separate
solvent accessible patches from those hidden ( and presumably less relevant )
but I can't quite make a database that can be reasonably queried for biologically 
similar components ( like cavities for example).



Thanks. 

> Date: Wed, 28 May 2008 09:56:18 +0800
> From: silkhuang at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] how pdb ID is defined?
>
>
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