cDNA-PDB mapping

Kristian Rother krother at chemie.fu-berlin.de
Sun Dec 24 13:33:28 EST 2000


Dear Iddo,

> I am well
> aware of ISSD, but it seems to be rather small.

And it does not seem to be up to date, either.
Recently, I had the same problem. After two weeks, I abandoned the
experiment
for this problem was growing too large to fit into a two-month practical
course.

I think someone might have to write something new that finds the best
matches between
Swiss-Prot and Pdb. That would really improve a lot of studies.


> Or, if someone has written any code which does that, and is willing to
> share, that will be great too.

I have written some classes that read and write PDB data in Java and
Python.

The code cares for the atomic coordinates most. Actually, organism and
molecule information 
is still ignored. 

You can find the latest version of both on:

http://userpage.chemie.fu-berlin.de/~krother/bioinf/protein.html
or
http://www.mandalay.de.vu (main page)

(Unfortunately, its all in German, Sorry)

Let me know if You want to something with the code, I might give some
additional advice.

Kristian







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