相关论文: De Novo Design of Protein-Binding Peptides by Quan…
Quantum annealing has the potential to find low energy solutions of NP-hard problems that can be expressed as quadratic unconstrained binary optimization problems. However, the hardware of the quantum annealer manufactured by D-Wave…
Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…
Benchmarking Quantum Process Units (QPU) at an application level usually requires considering the whole programming stack of the quantum computer. One critical task is the minor-embedding (resp. transpilation) step, which involves…
The D-Wave adiabatic quantum annealer solves hard combinatorial optimization problems leveraging quantum physics. The newest version features over 1000 qubits and was released in August 2015. We were given access to such a machine,…
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino…
Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in {\em in silico} materials design and drug discovery. In this paper, we propose a variable neighbourhood search…
Commercial adiabatic quantum annealers have the potential to solve important NP-hard optimization problems efficiently. The newest generation of those machines additionally allows the user to customize the anneal schedule, that is, the…
Quantum computing promises to speed up some of the most challenging problems in science and engineering. Quantum algorithms have been proposed showing theoretical advantages in applications ranging from chemistry to logistics optimization.…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Quantum annealing aims to solve combinatorial optimization problems mapped on to Ising interactions between quantum spins. A critical factor that limits the success of a quantum annealer is its sensitivity to noise, and intensive research…
Quantum annealing technologies aim to solve computational optimization and sampling problems. QPU (Quantum Processing Unit) machines such as the D-Wave system use the QUBO (Quadratic Unconstrained Binary Optimization) formula to define…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
Quantum optimization is the most mature quantum computing technology to date, providing a promising approach towards efficiently solving complex combinatorial problems. Methods such as adiabatic quantum computing (AQC) have been employed in…
Quantum annealing algorithms belong to the class of metaheuristic tools, applicable for solving binary optimization problems. Hardware implementations of quantum annealing, such as the quantum annealing machines produced by D-Wave Systems,…
The Fermi-Hubbard model (FHM) on a two dimensional square lattice has long been an important testbed and target for simulating fermionic Hamiltonians on quantum hardware. We present an alternative for quantum simulation of FHMs based on an…
One of the main challenges in drug discovery is to find molecules that bind specifically and strongly to their target protein while having minimal binding to other proteins. By predicting binding affinity, it is possible to identify the…
There have been multiple attempts to demonstrate that quantum annealing and, in particular, quantum annealing on quantum annealing machines, has the potential to outperform current classical optimization algorithms implemented on CMOS…
A quantum annealer heuristically minimizes quadratic unconstrained binary optimization (QUBO) problems, but is limited by the physical hardware in the size and density of the problems it can handle. We have developed a meta-heuristic solver…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…