Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration

Quantum Physics arXiv:2512.12573 (quant-ph) [Submitted on 14 Dec 2025] Title:Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration Authors:Pei-Kun Yang View a PDF of the paper titled Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration, by Pei-Kun Yang View PDF Abstract:Classical molecular docking is fundamentally constrained by the combinatorial growth of ligand translational and rotational degrees of freedom, rendering exhaustive pose enumeration infeasible on classical hardware. This work introduces a quantum-native formulation that encodes ligand occupancy on discretized three-dimensional grids and coherently generates the full ensemble of spatial configurations within a single quantum state. Multi-step translations and rotational transformations are controlled by ancillary qubits, enabling all symmetry-related configurations to be activated simultaneously. This framework provides a scalable foundation for quantum-accelerated virtual screening and is amenable to integration with quantum scoring approaches as quantum hardware continues to advance. Subjects: Quantum Physics (quant-ph) Cite as: arXiv:2512.12573 [quant-ph] (or arXiv:2512.12573v1 [quant-ph] for this version) https://doi.org/10.48550/arXiv.2512.12573 Focus to learn more arXiv-issued DOI via DataCite (pending registration) Submission history From: Pei-Kun Yang [view email] [v1] Sun, 14 Dec 2025 06:39:21 UTC (432 KB) Full-text links: Access Paper: View a PDF of the paper titled Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration, by Pei-Kun YangView PDF view license Current browse context: quant-ph new | recent | 2025-12 References & Citations INSPIRE HEP NASA ADSGoogle Scholar Semantic Scholar export BibTeX citation Loading... BibTeX formatted citation × loading... Data provided by: Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) Links to Code Toggle Papers with Code (What is Papers with Code?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)