A hybrid quantum-classical computing approach streamlines complex calculations by reformulating a key challenge in drug discovery: identifying how molecules bind to target proteins. This new method tackles molecular docking by transforming it into a graph-based problem solvable with advanced encoding techniques; this allows for more efficient use of computational resources while maintaining key optimisation structures. A new computational method has been devised for molecular docking, integrating both classical and quantum computing techniques to identify how molecules bind to target proteins. The team reformulated complex calculations as a graph-based problem, simplifying the search for optimal molecule arrangements within a protein’s binding site. The approach uses advanced encoding which efficiently represents information using qubits, the basic units of quantum information, reducing demand on processing power whilst preserving essential optimisation features. A new computational approach identifies how molecules bind to proteins, vital in designing effective drugs. Molecular docking requires immense computing power due to the sheer number of potential arrangements between drug candidates and their target proteins; it is like trying every possible key in a lock with billions of keys to test. The team reformulated this complex task as a graph-based problem, focusing on finding the most connected group within that network, akin to highlighting the biggest circle of friends where everyone knows each other. one hundred qubits molecular docking is a vital computational task in drug discoveryThe advancement provides a versatile platform to address increasingly intricate drug discovery challenges previously impossible due to substantial computing needs. Reformulating molecular docking as a graph-based combinatorial problem enabled efficient encoding with fewer resource demands while maintaining key optimisation structures vital for precise results. Employing a variational full-basis encoding strategy, representing data via Bloch sphere vectors, compressed information onto fewer qubits than conventional methods allowing execution on a superconducting quantum computer. Successful completion of docking