Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts?

Brennan-Tonetta²,

et al. 2021

SSRN Journal

There has been an increasing interest in and growing need for high performance computing (HPC), popularly known as supercomputing, in domains such as textual analytics, business domains analytics, forecasting and natural language processing (NLP), in addition to the relatively mature supercomputing domains of quantum physics and biology. HPC has been widely used in computer science (CS) and other traditionally computation intensive disciplines, but has remained largely siloed away from the vast array of social, behavioral, business and economics disciplines. However, with ubiquitous big data, there is a compelling need to make HPC technologically and economically accessible, easy to use, and operationally democratized.Therefore, this research focuses on making two key contributions, the first is the articulation of strategies based on availability, accessibility and usability for the demystification and democratization of HPC, based on an analytical review of Caliburn, a notable supercomputer at its inception. The second contribution is a set of principles for HPC adoption based on an experiential narrative of HPC usage for textual analytics and NLP of social media data from a first time user perspective. Both, the HPC usage process and the output of the early stage analytics are summarized. This research study synthesizes expert input on HPC democratization strategies, and chronicles the challenges and opportunities from a multidisciplinary perspective, of a case of rapid adoption of supercomputing for textual analytics and NLP. Deductive logic is used to identify strategies which can lead to efficacious engagement, adoption, production and sustained usage for research, teaching, application and innovation by researchers, faculty, professionals and students across a broad range of disciplines.

Section: Discussionmentioning

confidence: 99%

Strategies for Democratization of Supercomputing: Availability, Accessibility and Usability of High Performance Computing for Education and Practice of Big Data Analytics

Brennan-Tonetta²,

et al. 2021

SSRN Journal

Journal of Advanced Pharmaceutical Sciences

“…This allows the conduction of virtual screens for a massive number of molecules at an affordable cost. Cloud computing can replace local compute cluster used in research facilities saving the expenses of hardware, maintenance, and others (85)(86)(87) . Another advantage of VS techniques is the way the data is being processed to provide meaningful results.…”

Section: Cloud Computing and Deep Learning; The Future Of Vs Techniquesmentioning

confidence: 99%

Molecular docking and pharmacophore modelling; A bridged explanation with emphasis on validation

Mahrous,

Fathy,

Abu EL-Khair

et al. 2024

Virtual screening (VS) techniques have emerged in the past decade as an efficient strategy in lead identification. Molecular docking as well as pharmacophore and 3D-QSAR modelling are two major VS techniques standing out as cornerstones in the process of new drug discovery. Explanation of the mainvirtual screening techniques as well as the most commonly used validation parameters are discussed thoroughly emphasizing their use and shortcomings. Criteria for the selection of benchmarking datasets and training sets for molecular docking, pharmacophore, and 3D-QSAR models are discussed. Understanding the basics behind these techniques and their validation is crucial to judge the validity of the obtained results. Computational technologies have witnessed great improvement in the last few years which had a great impact on the improvement of virtual screening. Fields such as cloud computing and deep learning algorithms are among the technologies modeling the future of computer-aided drug design. This mini-review gives summarized knowledge for guiding beginners as well as experts in the field of virtual screening.

J. Pure Appl. Microbiol.

“…Combining curcumin and 10-undecenoic acid with existing antimicrobial agents such as antibiotics or biocides might contribute to restoring or enhancing their effectiveness against microbes. 87,86 Aswathanarayan and Vittal studied the biofilm inhibitory properties of berberine against Pseudomonas aeruginosa and Salmonella typhimurium. The phytochemical berberine is an isoquinoline alkaloid with tremendous inhibitory action on biofilm and, simultaneously, an excellent antibacterial and antiinfective compound.…”

Section: Phytochemicals As Quorum-sensing Inhibitorsmentioning

confidence: 99%

Bioprospecting and Exploration of Phytochemicals as Quorum Sensing Inhibitors against Cariogenic Dental Biofilm

Arya,

Usha

2024

Dental caries is a polymicrobial infection affecting the dental hard tissues. Excessive carbohydrate intake leads to the accumulation of acid-producing and acid-resistant microorganisms in the oral region. It is a biofilm-dependent oral infection with cariogenic pathogens and the most prevalent disease globally. The prevention and control of caries play a vital role in global health management. Periodontal diseases and subgingival plaque etiology are due to the combined action of bacterial invasion and immune reaction, resulting in the devastation of periodontal tissues, culminating in tooth loss. The compact micro colony inhabiting the dental surfaces attaches with secreted polymer, forming a biofilm. Bacterial biofilm impervious to various drugs and chemicals poses a significant challenge in therapeutic scenarios of medical and odonatological infections. The quorum-sensing signaling mechanism in bacteria controls the metabolic and physiologic properties involved in bacterial existence, pathogenesis, and virulence. Hence, studies monitoring the molecular mechanism of quorum sensing and their restricted social interactions will be highly beneficial in the treatment regimen of the modern era. Natural bioactive compounds can be exploited for their medicinal value in combating oro-dental infections. Phytochemicals are promising candidates that could provide novel strategies for fighting infections. The current review highlights the mechanism of quorum sensing, plant products’ effect in controlling quorum sensing, and biofilm-induced dental infections like Periodontitis.