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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…
Recent developments in the commercial open source community have catalysed the use of Linux containers for scalable deployment of web-based applications to the cloud. Scientific software can be containerized with dependencies, configuration…
This paper presents a comparative study of virtual machines (VMs) and containers for DevOps developers. The study explores the benefits and drawbacks of each technology in terms of their functionality, performance, security, and resource…
We propose a novel job scheduling approach for homogeneous cluster computing platforms. Its key feature is the use of virtual machine technology to share fractional node resources in a precise and controlled manner. Other VM-based…
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,…
The need for efficient computational screening of molecular candidates that possess desired properties frequently arises in various scientific and engineering problems, including drug discovery and materials design. However, the large size…
Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking…
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…
Underutilization of computing resources and high power consumption are two primary challenges in the domain of Cloud resource management. This paper deals with these challenges through offline, migration impact-aware, multi-objective…
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…
Deep learning has been postulated as a solution for numerous problems in different branches of science. Given the resource-intensive nature of these models, they often need to be executed on specialized hardware such graphical processing…
In this report we investigate the performance of Hadoop clusters, deployed with separated storage and compute layers, on top of a hypervisor managing a single physical host. We have analyzed and evaluated the different Hadoop cluster…
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…
In recent decades the analysis of data has become increasingly computational. Correspondingly, this has changed how scientific and statistical work is shared. For example, it is now commonplace for underlying analysis code and data to be…
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…
To improve system performance, modern operating systems (OSes) often undertake activities that require modification of virtual-to-physical page translation mappings. For example, the OS may migrate data between physical frames to defragment…
Linux containers have gained high popularity in recent times. This popularity is significantly due to various advantages of containers over Virtual Machines (VM). The containers are lightweight, occupy lesser storage, have fast boot-up…
2D materials find promising applications in next-generation devices, however, large-scale, low-defect, and reproducible synthesis of 2D materials remains a challenging task. To assist in the selection of suitable substrates for the…
Over the last few years, the use of virtualization technologies has increased dramatically. This makes the demand for efficient and secure virtualization solutions become more obvious. Container-based virtualization and hypervisor-based…
Heterogeneous computers integrate general-purpose host processors with domain-specific accelerators to combine versatility with efficiency and high performance. To realize the full potential of heterogeneous computers, however, many…