[Owl-devel] Residue contact potential

Jose M. Duarte jose.m.duarte at gmail.com
Thu Apr 15 06:30:56 EDT 2010

Hi AJ/Dan

Indeed the code we used in the lab for this is now public as Dan mentions.
Initially it started as a python project and this is the code that Dan is
talking about. Later we continued it as a pure java project and this is what
you can find now at http://www.bioinformatics.org/groups/?group_id=1014

If you like java surely you are welcomed to give it a go and even contribute
if you feel like it! The project is about analysing protein structures and
integrating different bioinformatics tools. In particular we have a lot of
code that deals with contact maps a.k.a. Residue Interaction Graphs. We have
implemented a fast algorithm for the computation of the contact maps that
you can use like this:

 Pdb pdb = new PdbfilePdb("/path/to/mypdbfile.pdb");
 RIGraph graph = pdb.getGraph("Ca",8);

That will get you a graph object that contains all the contacts for residues
whose Ca are <8A apart.

If you don't really want to get into all that you can always use the
genGraph command-line program that we provide. See a mini how-to I wrote on
this list some time ago:


With that you'll be able to get contact map files (simple text file with
some headers and 2 columns representing the i residue number and j residue
number) for contact types Ca or Cb and any distance cut-off.

Hope it helps


On 9 April 2010 16:31, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hi AJ,
> I hope your PhD is going well! I bet Cambridge is nice at the moment;
> are the magnolia trees out yet?
> I'm glad that the paper was of interest to you.
> To compile the data for the analysis I did, I used the tools and
> databases developed by colleagues while I was in the Structural
> Proteomics group in the Otto-Warburg-Laboratory at the Max Planck
> Institute for Molecular Genetics. The good news is that the group has
> decided to make those tools publicly available via an open source
> project at Bioinformatics.Org:
> http://www.bioinformatics.org/groups/?group_id=1014
> I have CC'ed this reply the open source mailing list for that group,
> where you can ask any questions about what you will need to get up and
> running. I have included my processing pipeline notes, and some basic
> scripts for your reference (see 'sample_files.tar.gz').
> JOSE: my python scripts say "from pypdb import Pdb"?
> Unfortunately it is often very hard to find simple software
> encapsulations of empirical potentials for protein scoring. This was
> the reason why I couldn't rigorously compare the potentials I
> developed to others in the literature.
> GREAT NEWS! I was just collecting the set of files for you to look at
> when I discovered I *have* created a 'stand alone' Perl program for
> calculating scores! (Terrible memory!)
> See the attached 'score_any_structure-2010.04.09.tar.gz'
> Let me know how you get on.
> All the best,
> Dan.
> P.S. Will you ask Madan when he will get NCI back up? It's been down for
> years!
> http://www.mrc-lmb.cam.ac.uk/genomes/nci/
> On 9 April 2010 14:26, A.J.Venkatakrishnan
> <venkatakrishnan.a.j at gmail.com> wrote:
> > Dear Dan,
> > Trust you are doing well. I am doing good, I started my PhD at the LMB
> under
> > Madan Babu and I am six months into it.
> > I recently came across your paper titled "Residue contact-count
> potentials
> > are as effective as residue-residue contact-type potentials for ranking
> > protein decoys" and it was a very interesting read. On a related note, I
> > would like to ask you for some advice.
> > I would like to compare the non covalent interaction energy between a
> given
> > pair of residues in different conformational states of a protein. I was
> > wondering if there is a software/program using which I could use to
> compute
> > residue-residue interaction potential given a protein structure.
> > Best,
> > AJ
> > --
> > --------------------------------------------
> > A.J.Venkatakrishnan
> > Ph.D. Student
> > St. Johns College
> > MRC Lab of Molecular Biology
> > University of Cambridge
> > --------------------------------------------
> >
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> Owl-devel at bioinformatics.org
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