Docking Box Size

Selecting an appropriate search space is critical to achieve high prediction accuracy in structure-based virtual screening. Therefore, we developed a procedure to customize the box size for individual query ligands in order to maximize the accuracy of molecular docking. Large-scale benchmarking calculations using AutoDock Vina the DUD-E dataset show that using the optimized box size improves the ranking accuracy in virtual screening. These results can help fully automate large-scale virtual screening calculations by customizing docking protocols on the fly for individual library compounds.
csb14
If you find our method useful, please cite the following paper:

 

Source codes

Version (hover) Download Size MD5  

 
1.1 latest eBoxSize-1.1.pl 4.1K 16f502a2756e721e770e6ca2569f8a13  
1.0 eBoxSize-1.0.pl 4.1K f40d1b434e760e91ab104156d6f86179  

 

Description

The Perl script eBoxSize.pl accepts ligands in PDBQT, SDF and MOL2 formats and returns a single number that is the optimal edge length of a cubic docking box.

[example]$ eBoxSize-1.1.pl nadp.pdbqt

28.738

Note that we recently re-optimized eBoxSize on a much larger dataset of pharmacologically relevant protein-drug complexes. The latest version (1.1) gives somewhat larger boxes yielding even better docking results.

Example

Below, we show how to use eBoxSize with Vina by self-docking NADP to aldose reductase (PDB-ID: 1adsA). The required input files are nadp.pdbqt (NADP) and aldr1.pdbqt (aldose reductase). Both files are in the PDBQT format. It is assumed that eBoxSize.pl and Vina are available from the search path.

[example]$ BOX_SIZE=$(eBoxSize-1.1.pl nadp.pdbqt)

[example]$ vina --receptor aldr1.pdbqt --ligand nadp.pdbqt --center_x 6.896 --center_y 0.784 --center_z 7.839 --size_x $BOX_SIZE --size_y $BOX_SIZE --size_z $BOX_SIZE --out aldr1-nadp.pdbqt --num_modes 1

PDB-bench dataset
Dataset Download Size MD5  

 
Target proteins PDB-bench.lst 22k 1f2e8decf7f4e73b14012f2edd2aeb30  

Target structures, ligand binding site predictions and other files for the PDB-bench and DUD-E datasets are available from the eFindSite datasets page.

 

© Michal Brylinski
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