Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers
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arXiv
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| Main Authors: | , , , , , , |
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| Format: | Preprint |
| Published: |
2024
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| _version_ | 1866908958282743808 |
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| author | Triuzzi, Emanuele Mengoni, Riccardo Micucci, Francesco Bonanni, Domenico Ottaviani, Daniele Beccari, Andrea Palermo, Gianluca |
| author_facet | Triuzzi, Emanuele Mengoni, Riccardo Micucci, Francesco Bonanni, Domenico Ottaviani, Daniele Beccari, Andrea Palermo, Gianluca |
| contents | Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by formulating the problem in QUBO terms, suitable for an annealing approach. We propose a problem formulation as a weighted subgraph isomorphism between the ligand graph and the grid of the target protein pocket. In particular, we applied a graph representation to the ligand embedding all the geometrical properties of the molecule including its flexibility, and we created a weighted spatial grid to the 3D space region inside the pocket. Results and performance obtained with quantum annealers are compared with classical simulated annealing solvers. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_06657 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers Triuzzi, Emanuele Mengoni, Riccardo Micucci, Francesco Bonanni, Domenico Ottaviani, Daniele Beccari, Andrea Palermo, Gianluca Biomolecules Computational Engineering, Finance, and Science Emerging Technologies Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by formulating the problem in QUBO terms, suitable for an annealing approach. We propose a problem formulation as a weighted subgraph isomorphism between the ligand graph and the grid of the target protein pocket. In particular, we applied a graph representation to the ligand embedding all the geometrical properties of the molecule including its flexibility, and we created a weighted spatial grid to the 3D space region inside the pocket. Results and performance obtained with quantum annealers are compared with classical simulated annealing solvers. |
| title | Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers |
| topic | Biomolecules Computational Engineering, Finance, and Science Emerging Technologies |
| url | https://arxiv.org/abs/2405.06657 |