DockEva 1.0.0

Calculating the Docking RMSD between two ligands

DockEva

DockEva: a fast open-source tool for atom mapping and docking evaluation of symmetric small molecules

Correctly comparing two poses of small molecule ligands with symmetry in fast is of significance important for the development of the related fields of receptor-ligand docking. Most of existing tools that correct for molecular symmetry do not consider the bonding structure of molecules, therefore resulting in non-physical atomic mapping. Using exhaustive algorithm to directly solve high sym-metry atom mapping problem is time-consuming. We present DockEva, a fast method for docking pose evaluation that converts the symmetry atom mapping problem to multiple maximum clique problems using the shortest road algorithm, in which the optimal atomic mapping and docking pose evaluation are performed in fast by solving the multiple maximum clique problems. Benchmarked results on decoys generated by AutoDock Vina demonstrate that DockEva can efficiently achieve the symmetry-corrected atom mapping with the minimum root mean square deviation (RMSD). Compared DockRMSD, one of the best existing methods for calculating RMSD of symmetric molecules, the average computational efficiency of DockEva (4.78×10^-3 seconds) is improved by about 6.36×10² times on the highly symmetric small molecules (their reasonable atom mapping numbers are all larger than 100) with more robust.

Pre-requisite:

- python

Installation:

On Linux/MacOS system:

  $ pip install DockEva

On Windows system:

  $ pip install DockEva

Example usage:

  $ DockEva path/to/crystal.mol2 path/to/decoy.mol2

For more example usages and options, try

  $ DockEva -h

Example output:

Check https://zhanglab.comp.nus.edu.sg/DockEva/ for an example output

Release History:

• First release 2024-10-14

Tips

• This package is free for all users. If you have any question, please email Jun Hu: [e-mail]

References

[1] Jun Hu, Jiawen Li, Yang Zhang. DockEva: a fast open-source tool for atom mapping and docking evaluation of highly symmetric molecules. sumitted.