ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways

Minh Khoa Nguyen (1) , Léonard Jaillet (1) , Stephane Redon (1)

1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems

This article proposes a method to efficiently generate approximate ligand unbind-ing pathways. It combines an efficient tree-based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is com-putationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state-of-the-art approaches. We show that the method is time-efficient and produces pathways in good agreement with other state-of-the-art solutions. These paths can serve as first approximations that can be used, analyzed or improved with more specialized methods.

Mots clés: ligand unbinding pathway; motion planning; ART-RRT; dimension reduction; morphing

Domaines: Modélisation et simulation

Minh Khoa Nguyen, Léonard Jaillet, Stephane Redon. ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways. Journal of Computational Chemistry, 2018, 39 (11), pp.665-678. ⟨10.1002/jcc.25132⟩. ⟨hal-01973778⟩