AutoDock, AutoGrid and the MGLTools for Debian and Ubuntu Linux
There is a series of applications that are key to many in some special communities. The availability of such in Debian, with accompanying helper applications, may be sufficient reason to make people adopt Debian (or its decendents) as their next Operating System. One such application is AutoDock.
When we are speaking about AutoDock, we are speaking about many different things:
The ?AutoDockSuite: implementing the computation of a change in energy that is experienced when a ligand binds to a receptor. This is manifested in the Debian packages
[http://packages.qa.debian.org/a/autodocksuite.html autodock] - the computation
[http://packages.qa.debian.org/a/autodocksuite.html autogrid] - the preparation of a particular pocket for the computation
The ?AutoDockToolkit: the biological preparation of the receptor and the ligand, which comes in many many Debian packages that offer Python packages. Most known are
[http://packages.qa.debian.org/a/autodocktools.html autodocktools] - packaged separately to prepare a protein structure and the (candidate) ligand for docking
[http://packages.qa.debian.org/m/mgltools-vision.html vision] - packaged as mgltools-vision to graphically specify workflows for protein docking experiments.
So, Debian has all these packages, currently in Sid. The autobuilders for the non-free section have already agreed to accept the MGLTools' non-free packages. Autodock and -grid are already available for Ubuntu since hardy. The MGLTools might just no make it for intrepid. However, the Debian packages can be used without changes for Ubuntu, please consider to give them a try.
aptitude install autodocktools autodock autogrid
The Debianisation is maintained together with many others in the DebianMed SCM system.
Popularity-Contest
For an overview on the acceptance of this package, please refer to the popularity-contest page (http://popcon.debian.org). An aquivalent page exists for Ubuntu, but their not so comfortable user interface stimulates the preference of the shell as follows:
wget -O - http://popcon.ubuntu.com/by_vote.gz 2> /dev/null | gunzip | egrep 'autodock|mgltool' wget -O - http://popcon.debian.org/by_vote.gz 2> /dev/null | gunzip | egrep 'autodock|mgltool'
Acknowledgements
It should be noted, that the number of Ubuntu installations is higher (close to double) than those on Debian. My respect. Many thanks go to Charles Plessy for the wget Ubuntu GUI substite. External to Debian there is to thank:
- Andreas Mischinski for his support in proving that the packages work for Ubuntu Feisty onwards.
The upstream developers at [http://www.scripps.edu Scripps] for caring for the functionality of their work on Debian/Ubuntu and for these Linux distributions at large
The [http://www.knowarc.eu KnowARC] project and the [http://www.nordugrid.org ?NorduGrid]
Helping ?UpstreamThat said, the developers of AutoDock and the MGLtools need to defend the public money that goes into their development by indicating the distribution and acceptance of their work in the community. The availability of these packages are certainly in the strong interest of their public funding agencies, but please
- install the popularity-contest package, so your installation gets counted
register yourself as a user for [http://autodock.scripps.edu/downloads/autodock-registration autodock] (at http://autodock.scripps.edu/downloads/autodock-registration). The MGLTools don't have such a registration.
See also
Nice introduction to Debian/Ubuntu and AutoDock
[http://users.ox.ac.uk/~jesu1458/installation_of_autodock_on_ubuntu_linux/ Installation] (upstream's packages)
[http://users.ox.ac.uk/~jesu1458/docker/ Docking] (compatible with these Debian/Ubuntu packages)