You might want to explore also our commandline version of TRAPP (available for Linux):
command line version.
Please note modifications of the server in our
changes document.
The TRAPP webserver offers
- a range of tools to explore binding site motions ranging from local side chain fluctuations to global backbone motions
- analysis of the binding site dynamics in simulated protein motion trajectories or trajectories provided by the user
- a tool for tracking, analysis and visualization of protein cavity dynamics in an ensemble of protein structures or in protein trajectories
- detection of transient pockets and subpockets that may appear due to protein motion
- combined analysis of the protein sequence conservation and the variations of the physicochemical properties of a binding pocket
- assessment of the binding pocket druggability and its variation in simulated trajectories and visualization of the pocket regions that favorably contribute to the pocket druggability
TRAPP is not designed to identify all of a protein's binding pockets, but rather to trace changes in the spatial and physicochemical
properties of a specified pocket in a protein that may arise due to the protein's flexibility.
The methodology has been developed in the
Molecular and Cellular Modeling group
at Heidelberg Institute for Theoretical Studies and is described
here.
