8 papers
Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration
Pei-Kun Yang
Classical molecular docking is fundamentally constrained by the combinatorial growth of ligand translational and rotational degrees of freedom, rendering exhaustive pose enumeratio…
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…
Quantum Convolutional Neural Network with Nonlinear Effects and Barren Plateau Mitigation
Pei-Kun Yang
Quantum neural networks (QNNs) leverage quantum entanglement and superposition to enable large-scale parallel linear computation, offering a potential solution to the scalability l…
Quantum Machine Learning for Predicting Binding Free Energies in Structure-Based Virtual Screening
Pei-Kun Yang
In structure-based virtual screening, it is often necessary to evaluate the binding free energy of protein-ligand complexes by considering not only molecular conformations but also…
Comparative Evaluation of PyTorch, JAX, SciPy, and Neal for Solving QUBO Problems at Scale
Pei-Kun Yang
Quadratic Unconstrained Binary Optimization (QUBO) is a versatile framework for modeling combinatorial optimization problems. This study benchmarks five software-based QUBO solvers…
Quantum Convolution for Structure-Based Virtual Screening
Pei-Kun Yang
Structure-based virtual screening (SBVS) is a key computational strategy for identifying potential drug candidates by estimating the binding free energies (delta G_bind) of protein…