Thomas Down thomas at derkholm.net
Wed Apr 30 17:05:01 EDT 2003

Once upon a time, on a computer far far away, pierre KHOUEIRY wrote:
> Hi,
>     I'm developping a JAVA interface in wish a user enter  a
> PROTEIN name and the interface will connect to the internet, get the
> PROTEIN SEQUENCE and add it to a JEditorPane and get the 2D and 3D
> strucutre of this protein and show them in a JFrame.
> My question is the following:  HOW can i do to make this search on the
> internet and to get results needed ?

If you know the PDB code, then you can get the structure file
either directly from PDB:


or from varioious other web/ftp sites that offer PDB
entries.  Finding a PDB code from a name might be harder.
The only way I know of that's going to work right now
is to use a website which has a searchable version of
PDB -- for instance, srs.ebi.ac.uk.  But this is going
to mean lots of ugly HTML parsing, and isn't stable if the
HTML changes.

MOBY might be a reasonable interface for a service which
allows PDB to be searched by protein name:


but as far as I know, they don't have that particular service
running, so you'd have to do some work yourself to set it up,
or persuade someone else to run it for you.

The DAS protocol, as it stands at the moment, doesn't include
any searching facilities, so it isn't directly going to help
you here.


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