Related papers: A GPU-accelerated Molecular Docking Workflow with …
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…
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…
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…
COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preliminary phases by using computer simulations. In particular,…
Public cloud computing environments, such as Amazon AWS, Microsoft Azure, and the Google Cloud Platform, have achieved remarkable improvements in computational performance in recent years, and are also expected to be able to perform…
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…
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it…
Many existing scientific workflows require High Performance Computing environments to produce results in a timely manner. These workflows have several software library components and use different environments, making the deployment and…
This paper documents the experience improving the performance of a data processing workflow for analysis of the Human Connectome Project's HCP900 data set. It describes how network and compute bottlenecks were discovered and resolved during…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
Edge computing offers the distinct advantage of harnessing compute capabilities on resources located at the edge of the network to run workloads of relatively weak user devices. This is achieved by offloading computationally intensive…
High-performance computing platforms such as supercomputers have traditionally been designed to meet the compute demands of scientific applications. Consequently, they have been architected as producers and not consumers of data. The Apache…
Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
High-throughput computational materials discovery has promised significant acceleration of the design and discovery of new materials for many years. Despite a surge in interest and activity, the constraints imposed by large-scale…
The increasing availability of cloud computing services for science has changed the way scientific code can be developed, deployed, and run. Many modern scientific workflows are capable of running on cloud computing resources. Consequently,…
Hybrid quantum-classical workflows combine quantum processing units (QPUs) with classical hardware to address computational tasks that are challenging or infeasible for conventional systems alone. Coordinating these heterogeneous resources…
Cloud-native is an approach to building and running scalable applications in modern cloud infrastructures, with the Kubernetes container orchestration platform being often considered as a fundamental cloud-native building block. In this…
Progress in science is deeply bound to the effective use of high-performance computing infrastructures and to the efficient extraction of knowledge from vast amounts of data. Such data comes from different sources that follow a cycle…
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…