Easily define the system and specify the search domain. Find ligand unbinding pathways from the active site of a receptor in a matter of minutes thanks to the novel ART-RRT method. Select the best pathways and apply further improvements to them (see Next steps).

Documentation

See the Ligand Path Finder tutorial for more information.

Next steps

To create pathlines for visualization of the movement of the center of mass of a ligand you can use the Pathlines app.

The resulting paths can be significantly improved with the help of the parallel Nudged Elastic Band (NEB) method implemented in the P-NEB app.

The resulting paths can be saved in the .sam and .samx formats. If you want to export only trajectories of some atoms along the path, you can use the Export Along Paths app.

References

If you use this app, please cite:

M. K. Nguyen, L. Jaillet and S. Redon. ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways. Journal of Computational Chemistry. Volume 39, Issue 11, April 30, 2018, Pages 665-678.