[Bio-Linux] Announcing the Backport of Concavity from Ubuntu 13.04 to Biolinux 7

[Sasa Paporovic]

Announcing the Backport of Concavity from Ubuntu 13.04 to Biolinux 7

To summarize the content, here is a short list what will be to read here:

1. What is concavity?

2. What is the genealogy between Ubuntu 13.04 and Biolinux 7
(Could be skipped for fully informed people)?

3. What is a backport?

4. How to get it now?!

5.Can we get more backports for the newest software in bioinformatics?


If you are only interested in to get it working, this mail and mail 4 is important to you and the rest must not be read.

If you are interested in read about the future in Mail 5 it is better to read Mail 2 and Mail 3 first, before you start with Mail 5. 

For short:

Concavity is a slim command line program for predicting ligand binding sites of proteins.

What is that good for:

One of the major issues for drug development in any way is to have a clue what kind of substances could bound to a protein.

For in silico prediction on this(e.g with AutoDock4 or its successor autodock-vina) it is helpful to reduce the protein surface to just that parts where an interaction is possible at all. This are the ligand binding sites of a protein.

There are sevaral algorithms available for this. E.g. Ligsite, Surfnet or Pocket finder. or...
Also webservices are there, which can do the job:
LigsiteCS, QsiteFinder, CASTp,... other.

Concavity arises arround 2009(yes, we are a little bit slow) with a new algorithmic approach as can be seen in:

“Predicting Protein Ligand Binding Sites by Combining Evolutionary  Sequence Conservation and 3D Structure” by John A. Capra et al. , PLOS, 2009 

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000585

PDF available in open Access(right site download button).

!Concavity reaches up to 80% prediction success!

, which is remarkable more than the webservices like CASTp, QsiteFinder and Ligsite, as can be seen in Fig.4 on page 7 in the paper of Capra, cited above.

The best webserver prediction was up to 60%(precision).

Conclusion:

80% precision with concavity v.s. 60% precision with established methods.

=>That should be brought to the heart of the bioinformatics community.

I have felt free to do do that via backporting.

The concavity package is already available via software-center in Biolinux 7. 

!Important!

!The additional package conservation-code is available too. It do the precalculations that are needed for concavity to reach the 80% precision! 


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