arXiv:2606. 30551v1 Announce Type: cross Abstract: Calculation of binding energies for protein-ligand molecular systems requires accurate treatment of the electronic structure, a quantum chemistry problem that scales exponentially on classical hardware, while current quantum hardware remains too noisy for the required circuit depths.
arXiv:2607. 20585v1 Announce Type: cross Abstract: Sample-based Quantum Diagonalization (SQD), an extension of Quantum Selected Configuration Interaction (QSCI), has emerged as a promising hybrid quantum-classical paradigm for computing molecular ground state energies.
arXiv:2508. 02641v2 Announce Type: replace-cross Abstract: Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics.
arXiv:2604. 14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames.
arXiv:2607. 20943v1 Announce Type: cross Abstract: 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.
The paper introduces MCTH (Monte Carlo Tree Hallucination), an inference-only framework that performs all‑atom biomolecular sequence‑structure co‑design by treating pretrained folding and inverse‑folding models as black‑box operators. MCTH uses Monte Carlo Tree Search to allocate a fixed inference budget across competing design trajectories, incorporating model confidence, uncertainty, and cross‑expert consensus. Experiments across protein‑RNA, protein‑DNA, protein‑protein, and protein‑ligand design show that adaptive search outperforms simpler sampling strategies, and evaluations with AlphaFold3 and Chai‑1 demonstrate transferability beyond the search‑time oracle.
arXiv:2607. 05736v1 Announce Type: new Abstract: Molecular property prediction often relies on isolated data modalities, where continuous 3D graph neural networks (GNNs) struggle to efficiently capture long-range topological dependencies and exact macroscopic heuristics.
Budgeted Quotient-Residual Guidance (QRG) is an inference-time correction that enables quotient-based lead‑optimization objectives—such as distances, contacts, and anchored substructures—to be actively used with frozen pocket‑conditioned molecular diffusion models without retraining. QRG lifts quotient covectors to metric‑horizontal ambient directions and delivers them through a trust budget set by the sampler’s step norm, providing a closed‑form sampler‑budget update and a product‑budget split for section and residual controls. Experiments on frozen TargetDiff backbones show that QRG improves ligand‑generation quality on fragment growing, scaffold hopping, and linker design while preserving novelty and diversity.
arXiv:2607. 01362v1 Announce Type: cross Abstract: Quantum mechanical (QM) cluster models provide an effective framework for mechanistic studies of enzymatic reactions but remain computationally demanding.
arXiv:2607. 19519v1 Announce Type: cross Abstract: Most 3D properties relevant to molecular design, including free energies and shape descriptors, are $\textit{expectations}$ over the Boltzmann distribution over 3D configurations of a molecular graph.
arXiv:2607. 22549v1 Announce Type: new Abstract: Hybrid quantum-classical protein structure prediction depends strongly on Hamiltonian penalty weights, yet existing lattice-based workflows typically fix these coefficients by hand and evaluate only very short fragments in simulation.
arXiv:2607. 09737v1 Announce Type: cross Abstract: Molecular docking predicts how a small molecule binds to a protein and is a key bottleneck in drug discovery.
arXiv:2608. 02642v1 Announce Type: cross Abstract: Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort.