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q-bio.BM2025
QUBODock: A Pip-Installable QUBO Tool for Ligand Pose Generation
Pei-Kun Yang
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…
q-bio.BM2025
Leveraging Conformational Diversity for Enhanced Structure-Based Virtual Screening: Insights from Molecular Dynamics Simulations of HIV-1 Protease-Ligand Complexes
Pei-Kun Yang
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexi…