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Install helper applications
Detailed installation instructions for some of the programs that are interfaced by Biskit
- Local Blast
- Installing and testing local blast tools, databases and environment.
- HMMER
- Install hidden markov model sequence analysis tools.
- Pfam database
- Install Pfam database for HMMER
- PDB database
- Install local PDB database
- T-Coffee & Co
- Installing T-Cofee, ClustalW and SAP
- Prosa2003
- Installation of Prosa2003
- SurfaceRacer
- Installation of the surfrace program for the calculation of accessible surface areas and curvatures.
- Modeller
- Installing Modeller (version 8.2 ... 9.3)
- XPlor-NIH
- Quick instructions for installing XPlor-NIH.
- Fold-X
- Download and install Fold-X
- ICM-Browser
- ICM-Browser is the free version of Ruben Abagayan's ICM program. There is lots of interesting functionality in there. Biskit right now only wraps a single method -- the calculation of CAD (Contact Area Difference) as a better behaved alternative to the classic RMSD measure for structure comparison.
- DSSP
- DSSP is the standard program for identifying secondary structure elements in protein structures.
- MSMS
- Quick instructions for installing the msms program for molecular surface calculations.
- Epydoc
- We use Epydoc for building the API documentation of Biskit.
- Intervor
- 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).
- Amber
- Installing the Amber simulation package (Amber 12)
- Compilers
- Installing custom compilers
- TM-Align
- Install the TM-Align structure alignment program (Zhang and Skolnick 2003).
- Reduce
- Install the Reduce program for adding of hydrogens to proteins and nucleic acids (Word et al. 1999)
- VMD
- not strictly a helper application of Biskit, VMD is nevertheless a very useful and professional visualization program.
- DelPhi
- The classic program for the calculation of electrostatic potentials and electrostatic free energies.
