... in a nutshell

dxTuber is the first cavity detection tool that takes into account protein and cavity dynamics using solvent and protein residence probabilities derived from molecular dynamics (MD) simulations. dxTuber supports all MD packages that VMD can process.

dxTuber results can be exported in PDB format where each cavity is an individually selectable object of coherent voxels written as pseudo atoms, each holding the residence probability information, in the form of mass-weighted solvent densities encoded as formal b-factors.

It calculates pore and tunnel profiles along principal axis, furthermore cavity volumes and solvent densities can be directly extracted from the PDB files. Based on this data cavity statistics can be obtained easily.

dxTuber is licensed under the GPLv2

 

dxTuber v0.27

Latest changes:

  • [New feature] Detected cavities can now be devided into subcavities 
  • [New feature] User can now decide if solvent voxels overlapping protein voxels will be ignored or be detected as cavity (command line version only)

    dxTuber_cmd.py -p <protein.dx> -s <solvent.dx>  --overlap  --pmd 0.1 --smd 0.3

    --pmd 0.1 & --smd 0.3 thresholds create densities near solvent and protein VDW radii and will be more accurate than the published ones.

  • Bugfixes ... 
  • for more details check the changelog

 

Old Releases

Google code project page

Read more about dxTuber in our publication:

Raunest M, Kandt C (2011): dxTuber: Detecting Protein Cavities, Tunnels & Clefts Based on Protein and Solvent Dynamics Journal of Molecular Graphics and Modelling. 29(7): 895-905