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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…

Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…

Structure-based virtual screening (SBVS) is a promising in silico technique that integrates computational methods into drug design. An extensively used method in SBVS is molecular docking. However, the docking process can hardly be…

Convolution is one of the fundamental operations of deep neural networks with demanding matrix computation. In a graphic processing unit (GPU), Tensor Core is a specialized matrix processing hardware equipped with reduced-precision…

Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum…

We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…

The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…

To respond to the need of efficient training and inference of deep neural networks, a plethora of domain-specific hardware architectures have been introduced, such as Google Tensor Processing Units and NVIDIA Tensor Cores. A common feature…

Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are…

Despite the great popularity of virtual screening of existing compound libraries, the search for new potential drug candidates also takes advantage of generative protocols, where new compound suggestions are enumerated using various…

Computational docking is the core process of computer-aided drug design; it aims at predicting the best orientation and conformation of a small drug molecule when bound to a target large protein receptor. The docking quality is typically…

Vectors of data are at the heart of machine learning and data mining. Recently, vector quantization methods have shown great promise in reducing both the time and space costs of operating on vectors. We introduce a vector quantization…

Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary…

Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…

Modern drug discovery is often time-consuming, complex and cost-ineffective due to the large volume of molecular data and complicated molecular properties. Recently, machine learning algorithms have shown promising results in virtual…

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…

Coupled cluster with singles, doubles and perturbative triples (CCSD(T)) often provides ground state correlation energies within "chemical accuracy," but suffers from high computational cost and steep scaling with system size. We present a…

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…

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…

Virtual screening performance depends heavily on the chosen docking and scoring methods. Recent AI-based tools such as DiffDock and NMDN have reported strong benchmark results, but their practical utility on realistic,…