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Install helper applications
Filed under:
installation
Detailed installation instructions for some of the programs that are interfaced by Biskit
- TM-Align
- Install the TM-Align structure alignment program (Zhang and Skolnick 2003).
- DSSP
- DSSP is the standard program for identifying secondary structure elements in protein structures.
- SurfaceRacer
- Installation of the surfrace program for the calculation of accessible surface areas and curvatures.
- DelPhi
- The classic program for the calculation of electrostatic potentials and electrostatic free energies.
- Prosa2003
- Installation of Prosa2003
- Local Blast
- Installing and testing local blast tools, databases and environment.
- PDB database
- Install local PDB database
- T-Coffee & Co
- Installing T-Cofee, ClustalW and SAP
- Modeller
- Installing Modeller (version 8.2 ... 9.3)
- XPlor-NIH
- Quick instructions for installing XPlor-NIH.
- Epydoc
- We use Epydoc for building the API documentation of Biskit.
- Hex
- Hex is a rigid body protein-protein docking program which is ranking solutions based on (soft) shape and electrostatic complementarity. It uses (very) Fast-Fourier-Transformation in spherical coordinates to perform a systematic search through the whole orientation space (sampling millions of orientations).
- VMD
- not strictly a helper application of Biskit, VMD is nevertheless a very useful and professional visualization program.
- AmberTools 17
- AmberTools provides ptraj, reduce, tleap and other packages wrapped by Biskit
- Older instructions
- Installation instructions for deprecated tools or versions that are not any longer officially supported