Practical protein-pocket hydration-site prediction for drug discovery on a quantum computer

arXiv:2512.08390 · quant-ph, physics.bio-ph, physics.chem-ph · Submitted 2025-12-09 · Read on arXiv

quant-ph, physics.bio-ph, physics.chem-ph

Submitted: 2025-12-09

Updated: 2025-12-11

Code: https://github.com/dwavesystems/dwave-neal

Terminology

• Accuracy — 17× in this paper · explained in 1 episode
• QUBO Formulation — 8× in this paper · explained in 3 episodes
• Benchmark — 6× in this paper · explained in 2 episodes
• Quantum Approximate Optimization Algorithm — 6× in this paper
• Benchmarking — 3× in this paper · explained in 3 episodes
• Combinatorial Optimization — 3× in this paper · explained in 2 episodes
• Noisy Intermediate-Scale Quantum — 3× in this paper
• Quadratic Unconstrained Binary Optimization — 3× in this paper
• Computer-Aided Drug Discovery — 2× in this paper
• Hybrid Approach — 2× in this paper · explained in 4 episodes
• Objective Function — 2× in this paper · explained in 2 episodes
• Principal Component Analysis (PCA) — 2× in this paper · explained in 4 episodes
• Reference Interaction Site Model — 2× in this paper
• Adaptive Sampling — 1× in this paper · explained in 1 episode
• Consistency — 1× in this paper · explained in 3 episodes
• Core — 1× in this paper · explained in 2 episodes
• Diffusion Model — 1× in this paper · explained in 8 episodes
• Diffusion Models — 1× in this paper · explained in 6 episodes
• Gaussian Mixture Model — 1× in this paper
• Gaussian Mixture Model (GMM) — 1× in this paper · explained in 2 episodes
• Interpretability — 1× in this paper · explained in 15 episodes
• Many-Body Effects — 1× in this paper · explained in 2 episodes
• Physical Constraints — 1× in this paper · explained in 7 episodes
• Quantum Circuits — 1× in this paper · explained in 2 episodes
• Supplementary Information — 1× in this paper

Sources

• FlashMD: long-stride, universal prediction of molecular dynamics
• Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models
• Quantum Algorithm for Protein Side-Chain Optimisation: Comparing Quantum to Classical Methods
• Quantum Circuits for the Metropolis-Hastings Algorithm
• Integrated error-suppressed pipeline for quantum optimization of nontrivial binary combinatorial optimization problems on gate-model hardware at the 156-qubit scale
• Comparison of QAOA with Quantum and Simulated Annealing
• Quantum Approximate Optimization Algorithm: Performance, Mechanism, and Implementation on Near-Term Devices
• A Quantum Approximate Optimization Algorithm
• Solving boolean satisfiability problems with the quantum approximate optimization algorithm
• Threshold for Fault-tolerant Quantum Advantage with the Quantum Approximate Optimization Algorithm

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