Efficient Protein Ground State Energy Computation via Fragmentation and Reassembly

Abstract

Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current efforts focus on developing strategies to fragment larger molecules into computationally manageable subsystems. In this work, we propose a novel strategy to enable quantum simulation using existing quantum algorithms. Our approach involves fragmenting proteins into their corresponding amino acids, simulating them independently, and then reassembling them post-simulation while applying chemical corrections. This methodology demonstrates its accuracy by calculating the ground state energy of relatively small peptides through reassembling, achieving a mean relative error of only $0.00469 \pm 0.01071\%$. Future directions include investigating, with larger quantum computers, whether this approach remains valid for larger proteins.