Quantum Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice
Abstract
In this work, we present the first implementation of the face-centered cubic (FCC) lattice model for protein structure prediction with a quantum algorithm. Our motivation to encode the FCC lattice stems from our observation that the FCC lattice is more capable in terms of modeling realistic secondary structures in proteins compared to other lattices, as demonstrated using root mean square deviation (RMSD). We utilize two quantum methods to solve this problem: a polynomial fitting approach (PolyFit) and the Variational Quantum Eigensolver with constraints (VQEC) based on the Lagrangian duality principle. Both methods are successfully deployed on Eagle R3 (ibm_cleveland) and Heron R2 (ibm_kingston) quantum computers, where we are able to recover ground state configurations for the 6-amino acid sequence KLVFFA under noise. A comparative analysis of the outcomes generated by the two QPUs reveals a significant enhancement (reaching nearly a two-fold improvement for PolyFit and a three-fold improvement for VQEC) in the prediction and sampling of the optimal solution (ground state conformations) on the newer Heron R2 architecture, highlighting the impact of quantum hardware advancements for this application.
Cite
@article{arxiv.2507.08955,
title = {Quantum Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice},
author = {Rui-Hao Li and Hakan Doga and Bryan Raubenolt and Sarah Mostame and Nicholas DiSanto and Fabio Cumbo and Jayadev Joshi and Hanna Linn and Maeve Gaffney and Alexander Holden and Vinooth Kulkarni and Vipin Chaudhary and Kenneth M. Merz and Abdullah Ash Saki and Tomas Radivoyevitch and Frank DiFilippo and Jun Qin and Omar Shehab and Daniel Blankenberg},
journal= {arXiv preprint arXiv:2507.08955},
year = {2025}
}