scholarly journals Final Report Coupled In Silico Microbial and Geochemical Reactive Transport Models: Extension to Multi-Organism Communities, Upscaling, and Experimental Validation

2014 ◽  
Author(s):  
Derek R. Lovley
Keyword(s):  
In Silico ◽  
Reactive Transport ◽  
Experimental Validation ◽  
Final Report ◽  
Transport Models

scholarly journals Identification of Potential HCV Inhibitors Based on the Interaction of Epigallocatechin-3-Gallate with Viral Envelope Proteins

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1257
Author(s):  
Fareena Shahid ◽  
Noreen ◽  
Roshan Ali ◽  
Syed Lal Badshah ◽  
Syed Babar Jamal ◽  
...  
Keyword(s):  
Hepatitis C ◽  
In Silico ◽  
Experimental Validation ◽  
Homology Modelling ◽  
Viral Envelope ◽  
Screening Methods ◽  
Binding Affinities ◽  
Autodock Vina ◽  
Potential Inhibitors ◽  
Very High

Hepatitis C is affecting millions of people around the globe annually, which leads to death in very high numbers. After many years of research, hepatitis C virus (HCV) remains a serious threat to the human population and needs proper management. The in silico approach in the drug discovery process is an efficient method in identifying inhibitors for various diseases. In our study, the interaction between Epigallocatechin-3-gallate, a component of green tea, and envelope glycoprotein E2 of HCV is evaluated. Epigallocatechin-3-gallate is the most promising polyphenol approved through cell culture analysis that can inhibit the entry of HCV. Therefore, various in silico techniques have been employed to find out other potential inhibitors that can behave as EGCG. Thus, the homology modelling of E2 protein was performed. The potential lead molecules were predicted using ligand-based as well as structure-based virtual screening methods. The compounds obtained were then screened through PyRx. The drugs obtained were ranked based on their binding affinities. Furthermore, the docking of the topmost drugs was performed by AutoDock Vina, while its 2D interactions were plotted in LigPlot+. The lead compound mms02387687 (2-[[5-[(4-ethylphenoxy) methyl]-4-prop-2-enyl-1,2,4-triazol-3-yl] sulfanyl]-N-[3(trifluoromethyl) phenyl] acetamide) was ranked on top, and we believe it can serve as a drug against HCV in the future, owing to experimental validation.

scholarly journals Timescales for the development of methanogenesis and free gas layers in recently-deposited sediments of Arkona Basin (Baltic Sea)

2012 ◽  
Vol 9 (5) ◽  
pp. 1915-1933 ◽  
Author(s):  
J. M. Mogollón ◽  
A. W. Dale ◽  
H. Fossing ◽  
P. Regnier
Keyword(s):  
Organic Matter ◽  
Baltic Sea ◽  
Reactive Transport ◽  
Reaction Pathway ◽  
Organic Matter Degradation ◽  
Muddy Sediment ◽  
Transport Models ◽  
Methane Gas ◽  
Geochemical Profiles ◽  
Arkona Basin

Abstract. Arkona Basin (southwestern Baltic Sea) is a seasonally-hypoxic basin characterized by the presence of free methane gas in its youngest organic-rich muddy stratum. Through the use of reactive transport models, this study tracks the development of the methane geochemistry in Arkona Basin as this muddy sediment became deposited during the last 8 kyr. Four cores are modeled each pertaining to a unique geochemical scenario according to their respective contemporary geochemical profiles. Ultimately the thickness of the muddy sediment and the flux of particulate organic carbon are crucial in determining the advent of both methanogenesis and free methane gas, the timescales over which methanogenesis takes over as a dominant reaction pathway for organic matter degradation, and the timescales required for free methane gas to form.

scholarly journals In silico identification and experimental validation of hits active against KPC-2 β-lactamase

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0203241 ◽  
Author(s):  
Raphael Klein ◽  
Pasquale Linciano ◽  
Giuseppe Celenza ◽  
Pierangelo Bellio ◽  
Sofia Papaioannou ◽  
...  
Keyword(s):  
In Silico ◽  
Experimental Validation ◽  
In Silico Identification
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