scholarly journals Computational toxicology, friend or foe?

2015 ◽  
Vol 4 (5) ◽  
pp. 1159-1172 ◽  
Author(s):  
Nigel Greene ◽  
William Pennie

Computational approaches offer the attraction of being both fast and cheap to run being able to process thousands of chemical structures in a few minutes. As with all new technology, there is a tendency for these approaches to be hyped up and claims of reliability and performance may be exaggerated. So just how good are these computational methods?

2021 ◽  
Author(s):  
Suzanne Ackloo ◽  
Rima Al-awar ◽  
Rommie E. Amaro ◽  
Cheryl H. Arrowsmith ◽  
Hatylas Azevedo ◽  
...  

Computational approaches in drug discovery and development hold great promise, with artificial intelligence methods undergoing widespread contemporary use, but the experimental validation of these new approaches is frequently inadequate. We are initiating Critical Assessment of Computational Hit-finding Experiments (CACHE) as a public benchmarking project that aims to accelerate the development of small molecule hit-finding algorithms by competitive assessment. Compounds will be identified by participants using a wide range of computational methods for dozens of protein targets selected for different types of prediction scenarios, as well as for their potential biological or pharmaceutical relevance. Community-generated predictions will be tested centrally and rigorously in an experimental hub(s), and all data, including the chemical structures of experimentally tested compounds, will be made publicly available without restrictions. The ability of a range of computational approaches to find novel compounds will be evaluated, compared, and published. The overarching goal of CACHE is to accelerate the development of computational chemistry methods by providing rapid and unbiased feedback to those developing methods, with an ancillary and valuable benefit of identifying new compound-protein binding pairs for biologically interesting targets. The initiative builds on the power of crowd sourcing and expands the open science paradigm for drug discovery.


2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.


2021 ◽  
Vol 21 (3) ◽  
pp. 1402-1423
Author(s):  
Harry Entebang ◽  
Swee-Kiong Wong ◽  
Zehnder Jarroop Augustine Mercer

The National Commodity Policy 2011-2020 was developed to increase the national income by harnessing the potential of commodity export revenues. Despite continuous efforts implemented by various related agencies, the overall performance of major commodities, particularly pepper, remains unsatisfactory. Regarded as a sought-after ‘king of spices’, pepper has become one of the most prized and important commodities traded globally. This paper highlights the development and performance of the pepper industry in Malaysia and discusses practical strategies and recommendations to transform the pepper industry. Besides conducting interviews with the industry experts to gain first-hand information, content and thematic analysis was employed based on secondary data research in this study. The findings of the study show that even though pepper is mostly used in food-related industries, its potential in pharmaceutical and cosmeceutical sectors remains underexplored. Globally, the overall supply and demand of pepper continue to increase, though the demand has recently exceeded supply. However, continuous new planting and farmexpansion initiatives by major producers caused the total global pepper supply to exceed consumption in 2018. In fact, pepper prices have declined more than 70% since 2015, which affected the overall household income of the rural community engaged in pepper farming. While experiencing low prices, smallholder pepper farmers and the industry continue to struggle with low domestic consumption, low production, higher cost of farm inputs, lack of extension services, low impact of research, development and innovation, ageing farming population, intense competition from other producing countries, low prices for quality pepper, limited subsidy to support continuous farming, pepper-related diseases, lack of new technology, and poor investment in downstream activities. Given this, the performance of the Malaysian pepper industry has fallen below expectations.


2021 ◽  
Vol 134 (7) ◽  
pp. jcs258594

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Asadullah and Sandeep Kumar are co-first authors on ‘Combined heterogeneity in cell size and deformability promotes cancer invasiveness’, published in JCS. Asadullah is a PhD Student in the lab of Prof. Shamik Sen at BSBE, IIT Bombay, Mumbai, India, who is interested in combining computational methods along with biophysics to study disease biology. Sandeep conducted the research described in this article while a PhD Student in Dr Shamik Sen's lab. He is now an Entrepreneur in Residence at TandemLaunch Inc., Montreal, Canada, interested in developing new computational approaches to studying development and cancer growth.


This exercises aims to familiarize students with chemical structures of natural products. Students will also use computational methods to learn about trends or the lack thereof in natural products.


2015 ◽  
Vol 2015 (1) ◽  
pp. 000079-000085 ◽  
Author(s):  
Michael Toepper ◽  
Tanja Braun ◽  
Robert Gernhardt ◽  
Martin Wilke ◽  
Piotr Mackowiak ◽  
...  

There is a strong demand to increase the routing density of the RDL to match the requirements for future microelectronic systems which are mainly miniaturization and performance. Photo-resists for structuring the metallization or acting as a mold for electroplating are common for very fine lines and spaces due to the developments in the front-end processing. For example chemical amplified Photo-resists are now moving in the back-end and wafer level packaging process. The results are mainly governed by the performance of the equipment i.e. the photo-tool. This is different for the permanent dielectric polymer material. The major difference in photo-resists and dielectric photo-polymer are the different functions of the material systems. Photo-resists are only temporary masks for subsequent process steps like etching and plating. This is different for the photo-polymers which are a permanent part of the future systems. In this paper a new technology is discussed which uses a laser scanning ablation process and BCB-Based Dry Film low k Permanent Polymer. Laser ablation of polymers is in principle not a new technology. Low speed and high cost was the major barrier. But the combination of a scanning technology together with quartz masks has opened this technology to overcome the limitation of the current photo-polymer process. The new technology is described in detail and the results of structuring BCB-Based Films down to less than 4 μm via diameter in a 15 μm thick film has been shown. The via side wall can be controlled by the fluence of the laser pulse. Test structures have been designed and fabricated to demonstrate the excellent electrical resistivity of the vias using a two-layer metallization process.


2001 ◽  
Vol 101 (7) ◽  
pp. 1981-2018 ◽  
Author(s):  
M. A. Peña ◽  
J. L. G. Fierro

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