Related papers: Exploiting OpenMP & OpenACC to Accelerate a Molecu…
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…
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…
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…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide…
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…
This documentation is designed for beginners in Graphics Processing Unit (GPU)-programming and who want to get familiar with OpenACC and OpenMP offloading models. Here we present an overview of these two programming models as well as of 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,…
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…
Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
Recent trends in the HPC field have introduced new CPU architectures with improved vectorization capabilities that require optimization to achieve peak performance and thus pose challenges for performance portability. The deployment of…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
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…
An increasingly large number of HPC systems rely on heterogeneous architectures combining traditional multi-core CPUs with power efficient accelerators. Designing efficient applications for these systems has been troublesome in the past as…
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…
Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…
Virtual screening (VS) is a computationally intensive process crucial for drug discovery, often requiring significant resources to analyze large chemical libraries and predict ligand-protein interactions. This study evaluates the…
Heterogeneity has become a mainstream architecture design choice for building High Performance Computing systems. However, heterogeneity poses significant challenges for achieving performance portability of execution. Adapting a program to…