QUBODock: A Pip-Installable QUBO Tool for Ligand Pose Generation
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arXiv
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| Format: | Preprint |
| Veröffentlicht: |
2025
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| _version_ | 1866908493159596032 |
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| author | Yang, Pei-Kun |
| author_facet | Yang, Pei-Kun |
| contents | We present QUBODock, a pip-installable tool that formulates ligand pose generation as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solves it efficiently on CPU or GPU. QUBODock focuses exclusively on pose generation and deliberately excludes any built-in scoring function, allowing researchers to pair its poses with external scorers of their choice. The software provides a minimal, reproducible interface for (i) protein-ligand structure ingestion and preprocessing, (ii) QUBO model construction from geometric/compatibility constraints, and (iii) decoding solutions into candidate poses for downstream ranking. Implemented in Python with GPU acceleration, QUBODock emphasizes usability and reproducibility: it is distributed on PyPI and can be installed with a single command. We release the source to support benchmarking, teaching, and method development around QUBO-based docking pose generation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_13014 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | QUBODock: A Pip-Installable QUBO Tool for Ligand Pose Generation Yang, Pei-Kun Biomolecules We present QUBODock, a pip-installable tool that formulates ligand pose generation as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solves it efficiently on CPU or GPU. QUBODock focuses exclusively on pose generation and deliberately excludes any built-in scoring function, allowing researchers to pair its poses with external scorers of their choice. The software provides a minimal, reproducible interface for (i) protein-ligand structure ingestion and preprocessing, (ii) QUBO model construction from geometric/compatibility constraints, and (iii) decoding solutions into candidate poses for downstream ranking. Implemented in Python with GPU acceleration, QUBODock emphasizes usability and reproducibility: it is distributed on PyPI and can be installed with a single command. We release the source to support benchmarking, teaching, and method development around QUBO-based docking pose generation. |
| title | QUBODock: A Pip-Installable QUBO Tool for Ligand Pose Generation |
| topic | Biomolecules |
| url | https://arxiv.org/abs/2508.13014 |