[Biojava-l] Protein Structure

[Thomas Down]

On Mon, Sep 10, 2001 at 04:32:40PM +0530, Nitin.Jain wrote:
> Hi,
> 
> I'm working on a tool which will display the 3D protein structures. I'm
> planning to make some classes which will encapsulate all the information
> available in PDB files, inculding the 3-Dimentional co-ordinates of each
> atom.
> Just to avoid re-inventing the wheel, I wanted to know if there are APIs
> already available in Bio-Java or other domain.

No, there isn't a 3d structure object model in BioJava
at the moment, although there has been a certain amount
of interest (we do, for instance, have a parser for PDB
files, contributed by the developers at Cambridge Antibody
Technology).

One direction you might try looking is the OMG's Life
Science Research division:

  http://lsr.ebi.ac.uk/

They're working on a standard set of interfaces for macromolecular
structure -- there may be an implementation of these that is
useful to you.  If not, they might be useful guidance for
designing your own API.

And if you /do/ decide to write your own, we'd be very interested
in including it in future versions of BioJava :-).



   Thomas.