[BiO BB] PDB vs MSD

[Dan Bolser]

One benifit of the MSD over the PDB is that it cleans and normalizes the
data, making links to secondary structure, taxonomy, uniprot, scop, cath,
pfam and ligand databases very easy (to mention a few).

Secondly it is built around the concept of a biomolecule, something which
is generated over an individual PDB file (which tipically contains only
the asymetrical unit in crystallographic terms).

Curently you need oracle to get independant access, or they can dump
custom queries for you. The API is good, but down last time I checked.
Last time I checked not all the data was correctly loaded, although that
may have changed. They have a nifty web query form, which you shouldn't
confuse with the PQS query pages at the MSD (group) website. PQS is
consumed by the MSD database (at the EBI, heh).

One criticism is that it is yet another pdb cleanup, including mmDB at the
NCBI and mmCIF at the PDB. There is no community consensus on the 'clean'
data. i.e. they are all potentially different.

I am a DB type person, so I like MSD a lot. I hope the current problems
are only teething problems (like where is the mysql version?), and this
could become a very powerfull tool for the community.



On Mon, 20 Sep 2004, sunita ahire wrote:

>Hi, can somebody tell me what are the differences betwwen PDB and MSD
>from database point of view(other than PDB is flat file and MSD is
>relational database). Any help is greatly appreciated.
> 
>Thanx in advance.
> 
>~Sunita
>
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