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Molecular docking is a crucial phase in drug discovery, involving the precise determination of the optimal spatial arrangement between two molecules when they bind. The such analysis, the 3D structure of molecules is a fundamental…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have…
Oscillator Ising Machines (OIMs) and probabilistic bit (p-bit)-based computing platforms have emerged as promising paradigms for tackling complex combinatorial optimization problems. Although traditionally viewed as distinct approaches,…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
The vast majority of 21st century AI workloads are based on gradient-based deterministic algorithms such as backpropagation. One of the key reasons for the dominance of deterministic ML algorithms is the emergence of powerful hardware…
Complex workflows play a critical role in accelerating scientific discovery. In many scientific domains, efficient workflow management can lead to faster scientific output and broader user groups. Workflows that can leverage resources…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning based methods are available to fulfil the docking task. The traditional docking methods are normally…
Neural quantum states efficiently represent many-body wavefunctions with neural networks, but the cost of Monte Carlo sampling limits their scaling to large system sizes. Here we address this challenge by combining sparse Boltzmann machine…
We experimentally demonstrate that the bias-field digitized counterdiabatic quantum optimization (BF-DCQO) algorithm, implemented on IonQ's fully connected trapped-ion quantum processors, offers an efficient approach to solving dense…
Ising machines can solve combinatorial optimization problems by representing them as energy minimization problems. A common implementation is the probabilistic Ising machine (PIM), which uses probabilistic (p-) bits to represent coupled…
Integrating quantum mechanics into drug discovery marks a decisive shift from empirical trial-and-error toward quantitative precision. However, the prohibitive cost of ab initio molecular dynamics has historically forced a compromise…
Quantum computing has gained a lot of attention recently, and scientists have seen potential applications in this field using quantum computing for Cryptography and Communication to Machine Learning and Healthcare. Protein folding has been…
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
In drug discovery, molecular docking aims at characterizing the binding of a drug-like molecule to a macromolecule. AutoDock-GPU, a state-of-the-art docking software, estimates the geometrical conformation of a docked ligand-protein complex…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
The development of tailored materials for specific applications is an active field of research in chemistry, material science and drug discovery. The number of possible molecules that can be obtained from a set of atomic species grow…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…