[Bio-Linux] Announcing the Backport of Concavity from Ubuntu 13.04 to Biolinux 7
Sasa Paporovic
sasa.paporovic at fh-bielefeld.de
Sat May 4 13:24:28 EDT 2013
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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