Introduction to DSXONLINE
DSXONLINE is a web-based user interface for the
knowledge-based scoring function DSX. DSXONLINE enables you to score
(putative) protein-ligand complexes of your interest, to browse and download the scoring
results, and to visualize the per-atom score contributions (see section
DSX pair potentials are derived in analogy the the DrugScore formalism developed by Gohlke et al. .
However, another set of atom types is used and contact types are clustered to circumvent problems with
the reference state. Torsion potentials and solvent accessible surface ratio potentials are
derived using the same formalism.
For more details see the upcoming publication which is currently in preparation.
For more consistence, DSX always assigns its own atom types and hydrogens are not regarded.
If you have ligand poses from a GOLD docking where water molecules were
included it is possible to consider the corresponding ON-marked waters in the solutions
Please note that there are even more options (like considering solutions from a docking
with flexible receptor residues) available in the DSX standalone version, which
will be freely available after publication.
- Visualization of the per-atom score contributions
The visualization of the per-atom score contributions is an intuitive way to
learn about differences between putative ligand geometries,
the effects of scaffold modifications or about the importance of certain
In the picture shown below, you find the visualization of the per-atom score
contributions of thrombin (deep blue, coated by the semi-transparent
molecular surface) and an in silico generated putative binding
geometry of its inhibitor melagatran (green) created with PyMOL .
Favorably interacting atoms are surrounded by blue spheres whereas
disfavorable interactions are shown in red. The sizes of the spheres
correspond to the values of the contributing per-atom scores. E.g. a large
blue sphere denotes a more attractive interaction than a small one, a large
red sphere stands for a more repulsive interaction than a small one.
Putative complex geometry of thrombin and melagatran
(click to enlarge)
We acknowledge the Cambridge Crystallographic Data Centre (CCDC) for making
the CSD data available to us.
We thank Dr. Hans Velec who implemented the original DrugScore-Online web pages and
whose PhP- and Python-Scripts were adapted for DSX-Online.
Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring-function to
predict protein-ligand interactions. J. Mol. Biol. 2000,
DeLano, W.L. The PyMOL Molecular Graphics System, DeLano Scientific, San
Carlos, CA, USA 2002.