ao9b01480_si_001.pdf (4.59 MB)
Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method
journal contributionposted on 2019-08-19, 13:43 authored by Kento Shin, Duy Phuoc Tran, Kazuhiro Takemura, Akio Kitao, Kei Terayama, Koji Tsuda
This paper proposes a novel molecular simulation method, called tree search molecular dynamics (TS-MD), to accelerate the sampling of conformational transition pathways, which require considerable computation. In TS-MD, a tree search algorithm, called upper confidence bounds for trees, which is a type of reinforcement learning algorithm, is applied to sample the transition pathway. By learning from the results of the previous simulations, TS-MD efficiently searches conformational space and avoids being trapped in local stable structures. TS-MD exhibits better performance than parallel cascade selection molecular dynamics, which is one of the state-of-the-art methods, for the folding of miniproteins, Chignolin and Trp-cage, in explicit water.