Personal tools
You are here: Home / Installing Biskit / Install helper applications

Install helper applications

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.
Reduce
Install the Reduce program for adding of hydrogens to proteins and nucleic acids (Word et al. 1999)
DelPhi
The classic program for the calculation of electrostatic potentials and electrostatic free energies.
Prosa2003
Installation of Prosa2003
Amber
Installing the Amber simulation package (Amber 12)
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
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.
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).
Compilers
Installing custom compilers
VMD
not strictly a helper application of Biskit, VMD is nevertheless a very useful and professional visualization program.