Molecular docking predicts how a small molecule binds to a protein and is a key bottleneck in drug discovery. Classical scoring functions sum empirical pairwise contacts, blind to quantum-mechanical effects like orbital charge transfer that govern binding specificity. We introduce Q-Score, encoding GNN-predicted orbital donor-acceptor energies into a weighted graph and scoring binding by solving a maximum-weight vertex clique problem via Digitized-Counterdiabatic QAOA. Each interaction anchor maps to one qubit and compatibility constraints become edges. Across 11 protein targets, DC-QAOA recovers the exact optimum on 8 at 10 qubits. On 1000 AI-generated molecules, Q-Score is orthogonal to classical scoring with Spearman rho of 0.05, driven by orbital quality with rho of 0.90, and free of molecular-weight bias, enriching for strong orbital interactions at twice the random rate. DC-QAOA achieves a mean approximation ratio of 0.94 with 52 percent exact. Execution of 1000 circuits on IBM Eagle confirms 6-qubit solvability on NISQ hardware.
Quantum Phase Estimation (QPE) is a foundational algorithm for molecular ground-state energy estimation, but its deep circuit requirements make direct hardware execution impractical on Noisy Intermediate-Scale Quantum (NISQ) devices. We present an analytically grounded variationa…
Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance. Here we present a systematic, compute-aware study of BO that evaluates surro…
Score-based diffusion models have achieved remarkable empirical success in generative modeling, yet their approximation-theoretic foundations remain incomplete. In particular, although classical universal approximation theorems guarantee that neural networks can approximate score…
We introduce implicit machine learning force fields (I-MLFFs), which replace explicit stacks of neural network layers with self-consistent fixed-point equations. In molecular simulations, this formulation enables intermediate representations to be reused across successive timeste…
Molecular glue degraders have emerged as a promising strategy for targeted protein degradation by inducing ternary complex formation between an E3 ubiquitin ligase and a target protein. Despite their therapeutic potential, computational design of molecular glues remains largely u…
We investigate a decentralized reinforcement learning problem involving multiple agents that interact with the same Markov Decision Process (MDP). The agents can exchange information over a network to collectively learn the optimal state-action value function. For this setting, w…