VMBiskit

The following packages are pre-installed on the virtual machine:

Note, that some of the above programs are distributed under non-free licenses that restrict their use to academic, non-commercial purposes. Study their license and use them at your own responsibility.

Other useful programs could not be bundled into vmbiskit because you need to explicitly register before using them. Apart from Amber (400 USD for an academic license), these are still "free for academic use" but cannot be freely distributed or adapted.

So, not yet installed are:

Xplor-NIH, in particular, is used a lot throughout Biskit and completes the docking pipeline implemented in Biskit.Dock. Amber also comes in handy for the docking protocol and is prereqiuisite for the conformational entropy calculations.

For space reasons, we also did not bundle any databases into the virtual machine. Before using the Hmmer-interface of Biskit (to map conservation profiles into a structure), you would need to install a local Pfam database (three easy steps). And before using the homology modeling pipeline, you also need to install local blast databases and the Modeller program (which again is excluded for license reasons).

Sorry about the inconvenience! This is a perfect demonstration how any license other than genuine Open Source restricts our freedom of research. Special thanks, nevertheless, to Charles Schwieter from the XPlor-NIH team and Yann Dublanche from the CRG. Charles tried hard to find a solution for bundling XPlor despite their license requirements; and Yann has experimented with a server for authenticated download.