My software notes

February 14, 2006

PDBSum announces topology diagrams for protein domains

Filed under: servers — kpwu @ 9:28 pm

NOTE (Nov.4th, 2011): I have made a new post showing how to generat such topology figure using online service provided by PDBSum.

Please click this post “[web server] protein structural analysis” to read new post.

 

domA01.gif

Like what you see above, it’s a protein topology diagram (sample: 1PJW.pdb). Starting on Feb Sixth, 2006, the PDBSum (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/)  announces the new service which provides the topology diagram of the coordinate file in Protein Data Bank (http://www.rcsb.org/pdb).

PDBsum intergrated many programs such as Procheck, WhatIF, Rasmol script and others. I really like the topology diagram generated by PDBSum, though I can’t find the source code from there. Hope they will release the source codes or compiled files for people who want to generate the topology diagrams of their fresh, before-submitting PDBs.

About these ads

4 Comments »

  1. i have not been able to generate these topology plots – have you?

    Comment by im confused — February 4, 2009 @ 9:50 am | Reply

  2. I think it’s still there. Choose one PDB (e.g. 1SVB), go to the “protein” tab on the top menu then you will see topology files for 4 domains.
    It should work fine for any other PDBs.

    Comment by kpwu — February 4, 2009 @ 1:48 pm | Reply

  3. i have my model homology modeling. I like to create these topology plot like that. can you suggest any software that can generate this look like topoology

    Comment by faizal — June 2, 2009 @ 11:57 pm | Reply

  4. Thanks for the useful note!
    It is useful even 7 years after you posted it.

    Thanks.

    Comment by RodAG_ — May 13, 2013 @ 1:02 am | Reply


RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

The Rubric Theme. Create a free website or blog at WordPress.com.

Follow

Get every new post delivered to your Inbox.

Join 31 other followers

%d bloggers like this: