Efficient molecular conformation generation with quantum-inspired algorithm

TL;DR

This paper introduces a quantum-inspired algorithm with a novel phase encoding method to efficiently generate molecular conformations, outperforming simulated annealing in speed while maintaining accuracy, demonstrating practical potential before quantum hardware matures.

Contribution

The paper presents a highly-compact phase encoding technique for quantum-inspired algorithms, significantly reducing representation space and improving conformation generation efficiency.

Findings

Root-mean-square deviation less than 0.5 Angstrom from DFT results

Median time-to-target reduced by a factor of five compared to SA

Successful simulation of QAOA reaching optimal results

Abstract

Conformation generation, also known as molecular unfolding (MU), is a crucial step in structure-based drug design, remaining a challenging combinatorial optimization problem. Quantum annealing (QA) has shown great potential for solving certain combinatorial optimization problems over traditional classical methods such as simulated annealing (SA). However, a recent study showed that a 2000-qubit QA hardware was still unable to outperform SA for the MU problem. Here, we propose the use of quantum-inspired algorithm to solve the MU problem, in order to go beyond traditional SA. We introduce a highly-compact phase encoding method which can exponentially reduce the representation space, compared with the previous one-hot encoding method. For benchmarking, we tested this new approach on the public QM9 dataset generated by density functional theory (DFT). The root-mean-square deviation between the conformation determined by our approach and DFT is negligible (less than about 0.5 Angstrom), which underpins the validity of our approach. Furthermore, the median time-to-target metric can be reduced by a factor of five compared to SA. Additionally, we demonstrate a simulation experiment by MindQuantum using quantum approximate optimization algorithm (QAOA) to reach optimal results. These results indicate that quantum-inspired algorithms can be applied to solve practical problems even before quantum hardware become mature.