eBoxSize

 
 
standalone
 

Selecting an appropriate search space is critical to achieve the high prediction accuracy in structure-based virtual screening. eBoxSize calculates an optimal box size for a query ligand in order to maximize the accuracy of molecular docking. Large-scale benchmarking calculations with AutoDock Vina against the DUD-E dataset show that employing the optimized box size improves the ranking accuracy in virtual screening.

  
eBoxSize
If you use eBoxSize, please cite the following paper:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.