Quantum Models
Quantum algorithms for molecular simulation and fold optimization.
Quantum Computing Fundamentals
DeutschโJozsa, BernsteinโVazirani, Simon's, Grover's, teleportation, superdense coding, QFT, QPE, Shor's code โ load any of them straight into the Circuit Composer
๐งฌ Category 1: Structural Biology & Biomolecular Folding
Encoding peptide structure as quantum Hamiltonians
Quantum Fold
Classical computers cannot efficiently solve protein folding at scale. Our quantum algorithm encodes peptide structure as a Hamiltonian and finds the lowest-energy conformation using VQE โ validated on IBM's 20-qubit quantum hardware.
Engine
qiskit-aer-local
Hardware
Quantum Simulator
GroveFold โ Grover Protein Design
Uses Grover's search algorithm to solve the protein design problem โ finding optimal amino acid sequences for target structures. Achieves quadratic speedup O(โN) over classical enumeration using custom pairwise energy tables with 8 amino acid types.
Engine
qiskit-grover
Hardware
IBM Quantum / Aer Simulator
๐ Khatami, Mendes, Wiebe, Kim (2022) โ arXiv:2201.12459 ย ยทย ๐ github.com/johnzl-777/GroveFold
PepFold โ QAOA Peptide Folding
Uses QAOA with an XY mixer on a 2D square lattice to sample the full conformational landscape of a peptide using the HP (Hydrophobic-Polar) binary model. Outputs a probability distribution over conformations โ not a single minimum โ revealing which folds are most likely. Validated against Boulebnane et al. 2023.
Engine
numpy-scipy-qaoa
Hardware
IBM Quantum / Aer Simulator
๐ Boulebnane et al. (2023) โ arXiv:2204.01821 ยท npj QI 9, 70 (2023) ย ยทย ๐ github.com/qiskit-community/quantum-protein-folding
Run Model โBF-DCQO Protein Folding
APRLRFY algorithmic validation on the 9-qubit tetrahedral Hamiltonian; not trapped-ion hardware reproduction.
Engine
Qiskit sampler
Hardware
Exact reference simulator
๐ Cadavid et al. (2025); Romero et al. (2025), arXiv:2506.07866
RNA Secondary Structure (QUBOโVQE)
Engine
qiskit / pennylane
Hardware
IBM Quantum (utility-scale)
๐ Mulligan et al. (2024) โ arXiv:2405.20328 (IBM ร Moderna)
Turn-Based 3D Coarse-Grained Folding
Engine
qiskit-gate / d-wave-qubo
Hardware
IBM + D-Wave Advantage
๐ arXiv:2311.14141, JCTC 2024
Quantum Protein Structure Prediction (QPSP)
Engine
qiskit-vqe
Hardware
Aer Simulator / IBM Quantum
๐ github.com/renatawong/quantum-protein-structure-prediction
Qiskit Community Reference Implementation
Engine
qiskit-ibm-runtime
Hardware
IBM Quantum (20-qubit)
๐ github.com/qiskit-community/quantum-protein-folding
QFold โ Quantum Reinforcement Learning
Engine
qiskit-rl-hybrid
Hardware
Hybrid / GPU Simulator
๐ github.com/roberCO/QFold
3D HP Lattice QUBO Folding
Engine
qubo-hybrid
Hardware
D-Wave / Qiskit Aer
๐ github.com/rajat709/Quantum-Protein-Folding
D-Wave Quantum Annealing Folding
Engine
d-wave-annealing
Hardware
D-Wave 2000Q
๐ Perdomo-Ortiz et al. (2012), Scientific Reports 2:571
QTank Gate-Based HP Folding
Engine
qiskit-gate-hp
Hardware
IBM Aer Simulator
๐ github.com/QTank/protein-folding
Hybrid QML Protein Folding
Engine
pennylane-qml
Hardware
Hybrid QML / GPU
๐ Papanikolaou (2023), NTUA Thesis
๐ Category 2: Drug Discovery & Molecular Design
Ligandโprotein binding, docking and virtual screening
DC-QAOA Molecular Docking
Digitized-counterdiabatic QAOA solves the maximum-vertex-weight clique formulation of molecular docking. The active 8SKH SARS-CoV-2 Mpro docking preset maps six compatible ligand poses to six qubits and recovers the highest-weight compatible pose set.
Preset
8SKH
Engine
QNG + Statevector
Problem
Weighted Clique
Based on: Ding et al. (2024) - Molecular docking via QAOA, arXiv:2308.04098
Run Model โQuantum Molecular Unfolding (D-Wave)
Engine
d-wave-annealing
Hardware
D-Wave Advantage
๐ Mengoni et al. (2021) โ arXiv:2107.13607
DC-QAOA Large Instance Docking
Engine
dc-qaoa-gpu
Hardware
GPU Cluster
๐ Papalitsas et al. (2025) โ arXiv:2503.04239
Neutral Atom Docking (VQAA)
Engine
pulser-neutral-atoms
Hardware
Pasqal / QuEra
๐ github.com/M-Garrigues/Quantum-Docking
QDock โ Quantum Docking Pipeline
Engine
qubo-hybrid
Hardware
D-Wave / IBM Quantum
๐ github.com/JinyinZha/QDock
Binding Affinity (VQE on Electronic Hamiltonians)
Engine
qiskit-nature / pennylane
Hardware
Aer Simulator
๐ Cao, Romero & Aspuru-Guzik (2018) โ doi:10.1147/JRD.2018.2888987
Virtual Screening (Grover)
Engine
qiskit
Hardware
Aer Simulator
๐ Hollenberg (2000) โ arXiv:quant-ph/0002076
โ Category 3: Quantum Chemistry & Molecular Simulation
Electronic-structure and Hamiltonian-dynamics simulation
Electronic-Structure VQE (UCCSD)
Engine
qiskit-nature / pennylane-qchem
Hardware
Aer Simulator
๐ Kandala et al. (2017) โ doi:10.1038/nature23879
Excited-State VQE (VQD / qEOM)
Engine
pennylane / qiskit-nature
Hardware
Aer Simulator
๐ Higgott, Wang & Brierley (2019) โ doi:10.22331/q-2019-07-01-156
Quantum Phase Estimation (QPE)
Engine
qiskit
Hardware
Aer Simulator
๐ Reiher et al. (2017) โ doi:10.1073/pnas.1619152114
Hamiltonian Simulation (Trotterization)
Engine
qiskit / cuda-q
Hardware
Aer Simulator
๐ Lloyd (1996) โ doi:10.1126/science.273.5278.1073
๐ Category 4: Pharmacology & ADMET Prediction
Quantum classifiers and regressors for drug-property prediction
Quantum Toxicity Classifier (VQC)
Engine
pennylane
Hardware
Aer Simulator
๐ Smaldone & Batista (2024) โ arXiv:2409.11269
Quantum ADMET Regression
Engine
pennylane
Hardware
Aer Simulator
๐ Batra et al. (2023) โ doi:10.1021/acs.jcim.3c01079
Quantum Kernel SVM (QSVM)
Engine
pennylane qml.kernels
Hardware
Aer Simulator
๐ Havlรญฤek et al. (2019) โ doi:10.1038/s41586-019-0980-2
๐งฌ Category 5: Genomics & Sequence Analysis
Sequence alignment, motif search and variant scoring
Quantum Sequence Alignment
Engine
pennylane / qiskit
Hardware
Aer Simulator
๐ Sarkar, Al-Ars & Bertels (2021) โ doi:10.3390/electronics10192433
Quantum Motif Search (Grover)
Engine
qiskit
Hardware
Aer Simulator
๐ Prousalis & Konofaos (2019) โ doi:10.1038/s41598-019-43697-3
Variant Effect Scoring (QAOA)
Engine
qiskit
Hardware
Aer Simulator
๐ Farhi, Goldstone & Gutmann (2014) โ arXiv:1411.4028
๐ค Category 6: Quantum Machine Learning for Biology
Quantum classifiers, kernels and generative models
Variational Quantum Classifier (VQC)
Engine
pennylane
Hardware
Aer Simulator
๐ Schuld et al. (2020) โ doi:10.1103/PhysRevA.101.032308
Quantum Kernel SVM (QSVM)
Engine
pennylane qml.kernels
Hardware
Aer Simulator
๐ Havlรญฤek et al. (2019) โ doi:10.1038/s41586-019-0980-2
Quantum Transfer Learning
Engine
pennylane + pytorch
Hardware
Aer Simulator
๐ Mari et al. (2020) โ doi:10.22331/q-2020-10-09-340
Quantum Generative Models (QGAN/QCBM)
Engine
pennylane / qiskit
Hardware
Aer Simulator
๐ Li et al. (2024) โ arXiv:2410.19425
Quantum Tensor Network (QTN)
Engine
pennylane
Hardware
Aer Simulator
๐ Huggins et al. (2019) โ doi:10.1088/2058-9565/aaea94
๐ธ Category 7: Biological Network Analysis
Gene networks, pathway enrichment and community detection
Disease Gene Prioritization (Quantum Walk)
Engine
pennylane / qiskit
Hardware
Aer Simulator
๐ Saarinen et al. (2024) โ doi:10.1093/bioinformatics/btae513
Graph Clustering / Community Detection (QAOA)
Engine
qiskit
Hardware
Aer Simulator
๐ Shaydulin et al. (2019) โ doi:10.1109/MC.2019.2908942
Pathway Enrichment (Grover)
Engine
qiskit
Hardware
Aer Simulator
๐ Grover (1996) โ arXiv:quant-ph/9605043
๐ฆ Category 8: Epidemiology & Population Health
Quantum walks and kernel methods for population-scale modeling
Quantum Epidemiological Modeling
Engine
qiskit
Hardware
Aer Simulator
๐ Kadian, Garhwal & Kumar (2021) โ doi:10.1016/j.cosrev.2021.100419
Population Structure (QSVM)
Engine
pennylane
Hardware
Aer Simulator
๐ Havlรญฤek et al. (2019) โ doi:10.1038/s41586-019-0980-2
๐ More quantum algorithms unlocking throughout 2026