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Helper applications
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 Executor.py. Program and environment settings are managed by ExeConfigCache.py. 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 |
|---|---|---|
| required: | ||
| 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 | |
| recommended: | ||
| pdb database | local PDB structure data base (folder with .ent files) | setup local PDB |
Biskit/Dock (protein-protein docking)
| program | purpose | link |
|---|---|---|
| required: | ||
| xplor | structure sampling | XPlor-NIH & setup xplor |
| HEX | fast protein-protein docking | HEX |
| SurfaceRacer | identify surface atoms | SurfaceRacer & setup surfrace |
| recommended: | ||
| 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 |