Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations. Results: We present a quantum-classical hybrid framework for simulating protein fragment electronic structure using variational quantum algorithms. We construct fermionic Hamiltonians from experimentally determined protein structures, map them to qubits via Jordan-Wigner transformation, and optimize ground state energies using the Variational Quantum Eigensolver implemented in pure Python. For a 4-orbital serine protease fragment, we achieve chemical accuracy (< 1.6 mHartree) with 95.3% correlation energy recovery. Systematic analysis reveals three-phase convergence behaviour with exponential decay (α = 0.95), power law optimization (γ = 1.21), and asymptotic approach. Application to SARS-CoV-2 protease inhibition demonstrates predictive accuracy (MAE=0.25 kcal/mol), while cytochrome P450 metabolism predictions achieve 85% site accuracy. Conclusions: This work establishes a pathway for quantum-enhanced biomolecular simulations on near-term quantum hardware, bridging quantum algorithm development with practical biological applications.
Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations. Results: We present a quantum-classical hybrid framework for simulating protein fragment electronic structure using variational quantum algorithms. We construct fermionic Hamiltonians from experimentally determined protein structures, map them to qubits via Jordan-Wigner transformation, and optimize ground state energies using the Variational Quantum Eigensolver implemented in pure Python. For a 4-orbital serine protease fragment, we achieve chemical accuracy (< 1.6 mHartree) with 95.3% correlation energy recovery. Systematic analysis reveals three-phase convergence behaviour with exponential decay (α = 0.95), power law optimization (γ = 1.21), and asymptotic approach. Application to SARS-CoV-2 protease inhibition demonstrates predictive accuracy (MAE=0.25 kcal/mol), while cytochrome P450 metabolism predictions achieve 85% site accuracy. Conclusions: This work establishes a pathway for quantum-enhanced biomolecular simulations on near-term quantum hardware, bridging quantum algorithm development with practical biological applications.
Variational quantum algorithms provide a direct, physics-based approach to protein structure prediction, but their accuracy is limited by the coarse resolution of the energy landscapes generated on current noisy devices. We propose a hybrid framework that combines quantum computation with deep learning, formulating structure prediction as a problem of energy fusion. Candidate conformations are obtained through the Variational Quantum Eigensolver (VQE) executed on IBM’s 127 qubit superconducting processor, which defines a global yet low resolution quantum energy surface. To refine these basins, secondary structure probabilities and dihedral angle distributions predicted by the NSP3 neural network are incorporated as statistical potentials. These additional terms sharpen the valleys of the quantum landscape, resulting in a fused energy function that enhances effective resolution and better distinguishes native like structures. Evaluation on 375 conformations from 75 protein fragments shows that, on this short fragment-only benchmark (10–14 residues without surrounding chain context), the hybrid pipeline achieves a mean RMSD of 4.9 Å with statistical significance ( p < 0.001), outperforming both quantum-only re-rankings and fragment-level runs of AlphaFold3 and ColabFold. We caution that this conclusion is restricted to the fragment-scale regime accessible to current quantum hardware and does not extend to the full-chain regime in which AlphaFold3 and ColabFold are usually evaluated. The findings demonstrate that energy fusion offers a systematic method for combining data driven models with quantum algorithms, improving the practical applicability of near term quantum computing to molecular and structural biology.
Protein structure prediction remains central to computational biology and drug discovery. While deep learning models such as AlphaFold have achieved remarkable accuracy for known fold families, they struggle with novel folds, intrinsically disordered regions, and conformational dynamics, and they do not explicitly optimize physics-based energy functions. We present a quantum-assisted approach to protein conformation optimization that uses parameterized quantum circuits within a variational framework to explore the energy landscape of small proteins and fragments from first-principles or coarse-grained physics. Our method encodes backbone torsion angles (ϕ, ψ) and selected side-chain degrees of freedom into qubit registers and employs a variational quantum eigensolver (VQE)-inspired optimization to minimize an approximate Hamiltonian incorporating bonded interactions, sterics, hydrogen bonding, and hydrophobic contacts. We introduce problem-inspired ansätze that respect chain connectivity and secondary-structure motifs (helices, beta-sheets) and propose hierarchical circuit growth strategies for scaling from peptides to larger domains. Through classical simulations of small peptides and secondary-structure motifs, we demonstrate that quantum variational optimization can identify low-energy conformations consistent with experimentally determined structures. We provide explicit resource estimates for NISQ and early fault-tolerant quantum computers and discuss hybrid classical-quantum strategies for refining quantum solutions with classical molecular dynamics and machinelearning priors. While full protein-folding quantum advantage remains distant, we identify concrete subproblems where nearterm quantum devices offer complementary physics-based insight beyond data-driven approaches, opening pathways toward practical quantum-classical protein structure and drug discovery pipelines.
Protein folding is a computationally intensive problem in bioinformatics that involves predicting the three-dimensional structure of a protein from its amino acid sequence. Classical approaches face challenges due to the exponential complexity of the search space. In this paper, we propose Q-ProteinFold, a quantum-classical hybrid system that leverages the Variational Quantum Eigensolver (VQE) for protein folding approximation. The system encodes protein sequences into parameterized quantum circuits using Qiskit and explores multiple conformations through quantum superposition and entanglement. A classical optimizer iteratively minimizes the energy function to identify stable protein structures. The implementation is developed using Python, Streamlit, and Qiskit Aer simulator. Experimental results demonstrate energy convergence, probabilistic state distribution, and effective fold prediction. This work highlights the potential of quantum computing in solving complex biological optimization problems.
Accurate prediction of protein active-site structures remains a central challenge in structural biology, especially for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a quantum computing framework designed for utility-level quantum processors to address this problem. Starting from an amino acid sequence, we cast structure prediction as a ground-state energy minimization task using the Variational Quantum Eigensolver (VQE). Amino acid connectivity is represented on a tetrahedral lattice, and steric, geometric, and chirality constraints are encoded into a problem-specific Hamiltonian expressed as sparse Pauli operators. A two-stage architecture separates energy estimation from measurement decoding, enabling noise mitigation under realistic device conditions. We evaluate the method on 23 real protein fragments from the PDBbind dataset and 7 fragments from therapeutically relevant proteins, executing all experiments on the IBM-Cleveland Clinic quantum processor. Structural predictions are benchmarked against AlphaFold3 (AF3) and classical simulation-based approaches using identical postprocessing and docking procedures. Our quantum framework outperforms both AF3 and classical baselines in Root-Mean-Square Deviation (RMSD) and docking efficacy, demonstrating a practical end-to-end pipeline for biologically relevant structure prediction on real quantum hardware and highlighting its engineering feasibility for near-term quantum devices.
Simulating strongly correlated molecular systems on near-term quantum hardware remains challenging because current hardware offers limited quantum volume and moderate-fidelity qubits. One way to address this challenge is through bootstrap embedding (BE). Bootstrap embedding partitions molecules into smaller fragments that are then embedded in the ``bath'' of other fragments iteratively. Bootstrap embedding is appealing for quantum simulation because fragmentation reduces the qubit requirements of each fragment problem. In this work, we develop a quantum bootstrap embedding (QBE) workflow that uses variational quantum eigensolver (VQE) fragment solvers and examines the algorithmic choices that determine the success of the overall VQE-QBE procedure. To improve efficiency, we introduce FastAdaptVQE, a sparse-matrix-accelerated form of the adaptive variational quantum eigensolver (ADAPT-VQE) that replaces symbolic commutator evaluation with direct statevector calculations, and MatrixFreeAdaptVQE, a matrix-free extension that removes the sparse-matrix memory bottleneck that arises for larger fragments. We also explore modifying the ADAPT-VQE operator-selection step by replacing the purely greedy choice with a lookahead strategy. Benchmarks on H4, F2, and selected geometries of H6 reach chemical accuracy, within 1 kcal/mol of BE results obtained with a full configuration interaction (FCI) solver. For n-butane, density-matching residuals converged, but energy errors remained outside chemical accuracy. These results show that combining QBE with VQE can accurately compute molecular energies, while density convergence alone does not ensure energy accuracy. This work lays the foundation for extending these energy calculations to larger molecular systems and quantum materials on near-term quantum hardware.
Abstract Quantum computing has emerged as a powerful tool for modeling molecular systems with high accuracy, accelerating the search for novel therapeutic targets. In this study, we present a two-stage hybrid workflow that combines a Quantum Graph Neural Network with a Variational Quantum Eigensolver to identify potent serine neutralizers in the QM9 dataset. In the first stage, an advanced quantum graph neural network architecture incorporating attention layers, self-distillation, and an adaptive learning-rate schedule is trained to predict ionization potentials and binding free energies. Across five independent random-seed trials, our adaptive-thresholded QGNN–VQE pipeline achieves an average R2 R 2 of 0.990±0.008 0.990 ± 0.008 and a mean absolute error of 0.034±0.001 0.034 ± 0.001 eV ( ≈0.79±0.03 ≈ 0.79 ± 0.03 kcal/mol) on the QM9 validation set, demonstrating robust, chemical-accuracy-level predictions. Building on these high-precision predictions, the second stage employs a QAOA-inspired hybrid ranking scheme that merges quantum graph neural network outputs, feature-space similarity (via and cosine similarity), and variational quantum eigensolver-derived energy stability. This α α -weighted ( α=0.95 α = 0.95 ) scoring framework is applied to over 133,000 molecules, efficiently parsed in parallel. The final ranked list is validated through an improved bijection test, featuring an adaptive similarity threshold to ensure both structural and functional robustness. The top-scoring candidate identified by our pipeline is 5,6,7-tetrahydro-4 H-pyrazolo[4,3-c]pyridin-4-one, highlighting the efficacy of quantum-enhanced modeling in pinpointing complex pharmacological targets. These findings underscore the transformative potential of hybrid quantum-classical workflows in drug discovery, offering a flexible blueprint for advanced screening of other critical biomolecular interactions in the rapidly expanding field of quantum biology. GraphicAbstract VQE for Serine Neutralization