Personal tools
You are here: Home / Installing Biskit / Helper applications

Helper applications

The list of third-party programs that can be used by Biskit

Biskit delegates many computational tasks to established programs written by other people. Some Biskit packages (like Mod) require certain programs in order to work at all. Others offer interfaces to certain programs for more specialised tasks. PDBDope, for example, can calculate a conservation profile for a protein if HMMER is installed -- if you can live without this particular functionality you dont need to install HMMER.

Note to developpers: New programs should be interfaced to biskit through subclasses of Program and environment settings are managed by Default settings for a program should be checked into Biskit/data/defaults/exe_yourprogram.dat*. Details are explained in the documentation of Executor, ExeConfig, and ExeConfigCache.

Install helper applications gives hints on the installation of the different programs.

Biskit base package

All optional:

program purpose comment or link
xplor PCR structure sampling we are switching to XPlor-NIH see also setup xplor
gbxplor   compiled for generalized Born
amber/sander multi-MD structure sampling Amber
amber/ptraj entropy calculations Amber
NCBI toolkit PDB cleaning NCBI tools see also setup local Blast
HMMER conservation profiles HMMER see also setup hmmer
pFam database profile database for Hmmer setup pFam database
SurfaceRacer surfaces and curvatures SurfaceRacer see also setup surfrace
MSMS surfaces MSMS (we prefer SurfaceRacer), see also setup MSMS
prosa2003 energy profiles Prosa2003 see also setup Prosa
DSSP secondary structure DSSP see also setup DSSP
foldX energy profiles Fold-X see also setup Fold-X
pymol visualisation PyMOL
icm_browser use CAD rather than RMS ICM Browser see also setup icmbrowser
TM-align structure alignment TM-align see also setup TM-align
reduce add hydrogens and optimize H-bonds see setup Reduce
DelPhi electrostatic free Energy PB solver see setup Delphi

Biskit/Mod (homology modelling)

program purpose link
blastall, fastacmd, blastclust   NCBI tools & setup local Blast
nr, pdbaa, sprot databases local sequence databases (formatted with -o) setup local Blast
t_coffee sequence alignments T-Coffee & setup T-Coffee
modeller   Modeller & setup Modeller
pdb database local PDB structure data base (folder with .ent files) setup local PDB

Biskit/Dock (protein-protein docking)

program purpose link
xplor structure sampling XPlor-NIH & setup xplor
HEX fast protein-protein docking HEX
SurfaceRacer identify surface atoms SurfaceRacer & setup surfrace
pymol visualisation PyMOL
prosa scoring Prosa2003 & setup Prosa
amber scoring / alternative sampling Amber
hmmer scoring by conservation HMMER & setup hmmer
foldX scoring Fold-X & setup Fold-X