Molecular Disassembly With Rrt-Like Algorithms

Abstract

This paper addresses the problem of computing pathways for a ligand to exit from the active site of a protein. Such problem can be formulated as a mechanical disassembly problem for two articulated objects. Its solution requires searching paths in a constrained high-dimensional configuration-space. Indeed, the ligand passageway inside the protein is often extremely cluttered so that current path planning techniques are unable to solve the disassembly problem in reasonable computing time. The techniques presented in this paper are based on the RRT algorithm. First we discuss some simple and general modifications of the basic algorithm that significantly improve its performance. Then we describe a new variant of the planner that treats ligand and protein degrees of freedom separately. This new algorithm outperforms the basic RRT, particularly for very constrained problems, and is able to handle models with hundreds of degrees of freedom. We analyze the effects of each RRT variant via several examples of different complexity. Although discussions and results of this paper focus on molecular models, the ideas behind the algorithms are general and can be applied to path planners for disassembling articulated mechanical parts.