Resource-Efficient Quantum Algorithm for Protein Folding

• Published in: arXiv.org
• Main Authors: Anton, Robert, Barkoutsos, Panagiotis Kl, Woerner, Stefan, Tavernelli, Ivano
• Format: Paper Journal Article
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 06.08.2019
• Subjects: Algorithms; Amino acids; Chemical properties; Computer simulation; Computers; Evolutionary algorithms; Fault tolerance; Folding; Genetic algorithms; Optimization; Organic chemistry; Physics - Quantum Physics; Protein folding; Proteins; Quantitative Biology - Biomolecules; Quantum computers; Quantum computing; Qubits (quantum computing)
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.1908.02163

Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine applications (e.g., in drug discovery) this subject has been intensively studied for over half a century. Although classical algorithms provide practical solutions, sampling the conformation space of small proteins, they cannot tackle the intrinsic NP-hard complexity of the problem, even reduced to its simplest Hydrophobic-Polar model. While fault-tolerant quantum computers are still beyond reach for state-of-the-art quantum technologies, there is evidence that quantum algorithms can be successfully used on Noisy Intermediate-Scale Quantum (NISQ) computers to accelerate energy optimization in frustrated systems. In this work, we present a model Hamiltonian with \(\mathcal{O}(N^4)\) scaling and a corresponding quantum variational algorithm for the folding of a polymer chain with \(N\) monomers on a tetrahedral lattice. The model reflects many physico-chemical properties of the protein, reducing the gap between coarse-grained representations and mere lattice models. We use a robust and versatile optimisation scheme, bringing together variational quantum algorithms specifically adapted to classical cost functions and evolutionary strategies (genetic algorithms), to simulate the folding of the 10 amino acid Angiotensin peptide on 22 qubits. The same method is also successfully applied to the study of the folding of a 7 amino acid neuropeptide using 9 qubits on an IBM Q 20-qubit quantum computer. Bringing together recent advances in building gate-based quantum computers with noise-tolerant hybrid quantum-classical algorithms, this work paves the way towards accessible and relevant scientific experiments on real quantum processors.