Scaling advantage of full-basis encoding for realistic docking graphs

Determine whether the qubit compression introduced by full-basis encoding continues to improve solution quality per physical qubit as molecular-docking binding interaction graphs become larger, denser, and more chemically realistic.

Background

The study demonstrates warm-start full-basis encoding (W-S FBE) on two moderate molecular-docking instances, for which exact classical verification remains possible. Full-basis encoding reduces the number of qubits by associating up to three classical variables with the three Bloch-vector components of each qubit, but the reported experiments do not establish how this compression behaves on substantially larger or more complex docking graphs.

The unresolved issue is whether reduced qubit usage will translate into better solution quality per physical qubit when the compatibility graphs include more vertices, denser constraints, and more chemically realistic interaction information. Resolving this question is identified as the decisive scaling test for the practical value of the encoding.