Related papers: GPU-Accelerated Drug Discovery with Docking on the…
The world has witnessed unprecedented human and economic loss from the COVID-19 disease, caused by the novel coronavirus SARS-CoV-2. Extensive research is being conducted across the globe to identify therapeutic agents against the…
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase…
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…
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…
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…
The emergence of COVID-19 has severely compromised the arsenal of antiviral and antibiotic drugs. Drug discovery is a multistep process with a high failure rate, high cost and it takes approximately 10-12 years for the development of new…
Today digital revolution is having a dramatic impact on the pharmaceutical industry and the entire healthcare system. The implementation of machine learning, extreme-scale computer simulations, and big data analytics in the drug design and…
Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…
Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric…
The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL)…
Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as…
Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…
In recent years, machine learning has been proposed as a promising strategy to build accurate scoring functions for computational docking finalized to numerically empowered drug discovery. However, the latest studies have suggested that…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…