Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration

TL;DR

This paper presents a quantum-native method for encoding and exhaustively enumerating ligand poses in 3D space, overcoming classical limitations through quantum superposition and control mechanisms.

Contribution

It introduces a novel quantum formulation that encodes ligand configurations on discretized grids, enabling simultaneous generation of all spatial arrangements within a single quantum state.

Findings

Enables exhaustive ligand pose enumeration using quantum encoding.

Provides a scalable framework for quantum-accelerated virtual screening.

Compatible with future quantum scoring methods.

Abstract

Classical molecular docking is fundamentally constrained by the combinatorial growth of ligand translational and rotational degrees of freedom, rendering exhaustive pose enumeration infeasible on classical hardware. This work introduces a quantum-native formulation that encodes ligand occupancy on discretized three-dimensional grids and coherently generates the full ensemble of spatial configurations within a single quantum state. Multi-step translations and rotational transformations are controlled by ancillary qubits, enabling all symmetry-related configurations to be activated simultaneously. This framework provides a scalable foundation for quantum-accelerated virtual screening and is amenable to integration with quantum scoring approaches as quantum hardware continues to advance.