The following packages are pre-installed on the virtual machine:
|numpy||fast numeric calculations in Python|
|Numeric||predecessor of numpy|
|biggles||advanced plotting in Python|
|pypvm||PVM-interface for Python|
|SurfaceRacer||surfaces and curvatures [see SurfaceRacer license]|
|MSMS||surfaces [see MSMS license]|
|DSSP||secondary structure analysis [see DSSP license]|
|NCBI toolkit||blast, blast_clust, (blast databases are not pre-installed)|
|HMMER||conservation profiles (the Pfam database is not pre-installed)|
|ICM-browser||use CAD rather than RMS|
|Hex||Protein-Protein docking [see Hex license]|
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||refinement, sampling, ..., see setup xplor|
|amber||structure sampling, entropy calculations, see Amber|
|modeller||homology modeling, see Modeller & setup Modeller|
|prosa2003||complex scoring, see Prosa2003 & setup Prosa|
|foldX||scoring, see Fold-X and setup Fold-X|
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.
(from the Serrano group server at the CRG)