Related papers: GPU-optimized Approaches to Molecular Docking-base…
Drug discovery is the most expensive, time demanding and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should…
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…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
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…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
GPUs offer massive compute parallelism and high-bandwidth memory accesses. GPU database systems seek to exploit those capabilities to accelerate data analytics. Although modern GPUs have more resources (e.g., higher DRAM bandwidth) than…
Similarity search finds application in specialized database systems handling complex data such as images or videos, which are typically represented by high-dimensional features and require specific indexing structures. This paper tackles…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
The recent introduction of powerful embedded graphics processing units (GPUs) has allowed for unforeseen improvements in real-time computer vision applications. It has enabled algorithms to run onboard, well above the standard video rates,…
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…
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,…
Many techniques in program synthesis, superoptimization, and array programming require parallel rollouts of general-purpose programs. GPUs, while capable targets for domain-specific parallelism, are traditionally underutilized by such…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
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…
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…
The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal…
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…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules…